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1. Lateral genetic exchange is a profound consequence of the co-existence of viruses (bacteriophages) and bacteria in freshwater ecosystems. Transduction is distinct from other mechanisms of genetic exchange because it is driven by potentially lethal agents external to the donor and recipient cells. Therefore, transduction is reputed to be a major driving force behind the diversity in natural populations and communities of bacteria. 2. Both generalized transduction (where every segment of the donor's genome has equal chance of being transferred to a recipient cell) and specialized transduction (where certain donor gene sequences are transferred at higher frequencies than others based on their proximity to the integration site of the transducing bacteriophage genome) have been demonstrated for various freshwater bacteria. However, these genetic exchange events occur at frequencies that vary widely, from 10−2 to 10−10 transductants per recipient, depending on the influence of various physical, chemical and biotic environmental factors on the outcome of phage–host encounters. Methodological constraints limit the interpretation of results from early studies of transduction in freshwaters because those studies introduced exogenous organisms in microcosms and excluded, to different extents, naturally occurring environmental conditions and their variability. 3. To assist the design and extrapolation of empirical observations, mathematical models including application of Group Theory are useful to estimate boundaries of the impact of transduction in generating and maintaining microbial diversity in freshwater. These theoretical excursions generate hypotheses and questions that can only be answered through refinement of current empirical estimates of transduction frequency, polarity of gene mobilization, bacteriophage host ranges, and the influence of gradients in environmental parameters that characterize freshwater ecosystems. [ABSTRACT FROM AUTHOR]

1. The goal of this study conducted in three lakes differing in nutrient content and size was to assess the temporal variation in viral community composition and possible co-variation with compositional changes in bacterial communities. 2. The viral community composition differed among lakes and changed over the season. Changes could also be detected on short-time scales, i.e. over a few days. These changes were comparable in magnitude to the changes detected between months or seasons. 3. The most important environmental factors co-varying with viral community composition, as determined by multivariate analysis, differed over the year and among lakes. Temperature and concentrations of dissolved organic carbon (DOC), total phosphorus and soluble reactive phosphorus were the most important factors. 4. Bacterial community composition also varied over the season and among lakes. The most important factors co-varying with bacterial community composition, as determined by multivariate analysis, were also temperature and DOC concentration. 5. Correlation between viral and bacterial community composition was weak and appeared to be a result of an indirect connection rather than a direct relationship between bacteria and viruses. [ABSTRACT FROM AUTHOR]

1. Viruses have been identified as an important component of plankton communities but their temporal dynamics remain poorly characterized, especially in littoral zones of lakes. Seasonal and diel dynamics of planktonic viruses and their main hosts (i.e. bacteria) were therefore assessed along four parallel transects of a lake, extending from within a littoral reed stand across the littoral shelf to the pelagic zone. 2. Viral abundance ranged from 1.9 to 9.7 × 107 virus-like particles (VLP) mL−1 with distinct seasonal peaks in spring at all locations. Seasonal variation in bacterial abundance varied more than 10-fold (0.85–12 × 106 cells mL−1) and was synchronized with changes in viral abundance. As a result, the ratio of viruses to bacteria (average of 12.5) varied much less over the year. 3. Bacterial production (0.11–0.98 μg C L−1 h−1) and growth rates (0.06–0.85 day−1) also varied seasonally but, in contrast to abundances, high production rates in spring were maintained in mid-summer, particularly in the reed stand, where growth rates were highest. 4. Variation among locations was small in most measured parameters, probably due to extensive exchange between pelagic and littoral water masses. Nevertheless, average bacterial growth and production rates in all seasons were consistently highest in the reed stand. 5. In the August of an exceptionally warm summer, viral and bacterial abundance varied little over a diel cycle (1.23–1.75 × 108 VLP mL−1 and 0.78–1.90 × 107 cells mL−1, respectively) in spite of a trend towards higher values at night. Diel changes in bacterial production (0.23–0.69 μg C L−1 h−1) and growth rate (0.02–0.06 day−1) were more pronounced, with higher values also occurring during the night, possibly indicating that bacterio- and phytoplankton production were not tightly coupled during our diel study. 6. Overall these results indicate that seasonal changes of virio- and bacterioplankton were mainly driven by high microbial activity in spring and were more pronounced than either diel changes on a hot summer day or spatial differences at a scale of 10–100 m. [ABSTRACT FROM AUTHOR]

1. Viruses in aquatic ecosystems can alter the abundance of bacteria and influence organic matter flows and bacterial community composition, but the combined effects of the multiple processes involved in the bacteria-mediated carbon cycle are not entirely clear. 2. We developed a new conceptual model that incorporates a fundamental but neglected aspect of bacteria–organic matter interactions: that different bacterial groups utilize different kinds of organic matter. In addition, the model incorporates several other realistic features of microbial food webs, including the presence of lysogenic viruses, bacterial resistance to viral infection and dependence of protozoan grazing rate on viral infection. 3. Our model analysis indicates that a ‘viral shunt’ view (i.e. viruses enhance bacterial utilization of organic carbon through regeneration of organic matter but diminish carbon flow to higher trophic levels) is robust, regardless of the specific situations we examined by either incorporating or ignoring various features of microbial food webs. 4. We also found that host-specific mortality induced by viral infection changes the bacterial utilization of different types of organic matter, which was attributable to diminished ‘apparent competition’ between predator-sharing bacterial groups that use different carbon sources. This mechanism can facilitate transformation to carbon dioxide of diverse types of carbon sources (e.g. organic matter of algal and terrestrial origin, methane or xenobiotics) and extends the previously recognized roles of viruses in microbial food webs. [ABSTRACT FROM AUTHOR]

1. The goals of this study were to assess which environmental gradients can be important in predicting viral abundance (VA), the frequency of virus-infected cells (FVIC) and burst size (BS), and to assess which lake characters favour viral-induced bacterial mortality (VBM) as opposed to potential grazer-induced bacterial mortality (PGBM). 2. The epilimnion and hypolimnion of 21 lakes differing in trophic status and humic content were investigated. Samples were obtained for viral and bacterial abundance, the FVIC and burst size, flagellate and ciliate abundances and water chemistry. The potential importance of VBM in relation to PGBM was calculated based on data on FVIC and flagellate and ciliate abundance. 3. Partial least squares regression (PLS) analysis showed that VA as well as the ratio between viral and bacterial abundance were positively related to inorganic nutrient concentrations, dissolved organic carbon concentration, chlorophyll- a concentration and bacterial production. 4. The PLS model also revealed that FVIC decreased with increasing trophic status whereas BS increased. Furthermore, potential grazing was positively related to increasing trophic status and decreasing humic content. PGBM appeared to be dominating over VBM in the majority of lakes sampled, especially in the epilimnion. 5. Thus, the relative importance of viruses for bacterial mortality was potentially highest in humic lakes of medium trophic status and it was also greater in the hypolimnion than in the epilimnion. [ABSTRACT FROM AUTHOR]

1. Viruses are a pervasive component of microbial food webs in both marine and freshwater systems. The abundance of viruses in individual aquatic systems appears to be independent of salinity but related to the biomass of primary and secondary producers as well as seasonal effects. Burst size, virus production rate and the percentage of microbial cells carrying a viral burden also appear to be more closely correlated to trophic status than to salinity. 2. In marine environments, the roles of planktonic viruses as regulators of carbon and nutrient cycling as well as microbial community structure have been a focus of numerous studies, yet the roles of freshwater virioplankton remain much less studied. Nevertheless, a survey of published freshwater studies demonstrates that virioplankton recycle important quantities of growth-limiting nutrients from hosts via generation of dead particulate and dissolved organic matter during cell lysis, and suggests that both the chemical speciation and concentration of these organic compounds and nutrients may have important influences on the microbial community. 3. Parallel observations on the spatial patterns and dynamics of microbial mortality due to viruses or grazing are more advanced in freshwaters than in marine environments. However, the constraints that determine whether virus- or grazer-mediated mortality dominates are not yet understood in either environment. 4. Application of molecular approaches has facilitated the examination of the diversity and ecological dynamics of specific viral populations and entire communities. The depth of detail achieved in marine environments towards characterizing these populations and communities is just beginning to be matched in freshwater systems. The few available data suggest that viruses targeting-related hosts in freshwater and marine systems may be genetically distinct. 5. Although the role of viruses in aquatic systems is complex and remains insufficiently studied, our survey of the literature indicates that, despite some differences, many of the controls on virioplankton activity and diversity are similar in marine and freshwater environments. [ABSTRACT FROM AUTHOR]

1. Viruses are the most abundant biological entities on the planet, and sediments provide a highly suitable environment for them. This review presents the first comparative synthesis of information on the fresh water and marine viriobenthos and explores differences and similarities to the better known virioplankton. We present methods for studying life cycles of the viriobenthos, data on viral distribution and diversity, interactions with host microbes, and information on the role of viruses in benthic food webs and biogeochemical cycles. 2. Most approaches developed for the virioplankton are also applicable to viriobenthos, although methods for analysing benthic viruses may differ in important details. 3. Benthic viruses are very abundant in both marine and freshwater sediments, where 107–1010 can occur in 1 g of dry sediment. Although information on viral production (VP) and decay rates in freshwater sediments is very limited, the data suggest that VP and decay could also be high. These data highlight the potential ecological importance of benthic viruses, suggesting that they could play a key role in prokaryotic mortality and in biogeochemical cycles. 4. There is clear indirect evidence for the importance of viriobenthos in marine and freshwater ecosystems. However, large numbers of visibly infected cells have not been observed, suggesting limited effects on prokaryote population and community dynamics. The apparent paradox between high viral abundance and low impact is currently unresolved, while several aspects of viral life cycles in sediments (e.g. chronic infection) are almost completely unknown. 5. Studies on viriobenthic diversity and community structure are at a pioneering stage. First results from a few studies using pulsed-field gel electrophoresis and especially from metagenomic analyses indicate, however, that viriobenthic assemblages are both highly diverse and distinct from the virioplankton. 6. Estimates of global viral abundance in the top 1 m of fresh water and marine sediments are 0.5 and 28.7 × 1028 viruses respectively. Similar rough estimates of production are 0.6 and 34.4 × 1028 viruses day−1, suggesting an average turnover time of 20 h. [ABSTRACT FROM AUTHOR]

1. Viruses have become widely recognized as the most abundant biological entities and important players in aquatic environments, and this realization has profoundly changed our conceptual understanding of the functioning and regulation of aquatic ecosystems in the last two decades. However, most of this research has focussed on marine viruses, especially in pelagic environments. 2. Here we introduce a special issue of Freshwater Biology dealing with viruses in freshwater ecosystems. It represents the first attempt to summarize progress in freshwater viral ecology made by diverse research groups and to direct attention of viral ecologists towards fresh waters. 3. Six review-type articles and ten original research papers cover a wide range of aspects of freshwater viral ecology. This includes reports on the distribution of freshwater viral communities in contrasting habitats (e.g. sediments, wetlands, littoral zone, open waters), on different roles of viruses in freshwater ecosystems (e.g. mortality rates of bacteria and phytoplankton, transduction, influence on bacterial diversity and organic matter), and on different types of viruses (bacteriophages, cyanophages, algal viruses, and a fish-pathogenic virus). 4. Collectively the series of papers presented in this special issue indicates that freshwater environments cover great habitat diversity and that the significance of some of the mechanisms controlling viral dynamics and impacts may differ between freshwater and marine habitats. [ABSTRACT FROM AUTHOR]