by Stephen T. Abedon

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1. Blum, H., W. Zillig, S. Mallock, H. Domdey, and D. Prangishvili. 2001. The genome of the archael virus SIRV1 has features in common with genomes of eukaryal viruses. Virology 281:6-9. abstract: The virus SIRV1 of the extremely thermophilic archaeon Sulfolobus has a double-stranded DNA genome similar in architecture to the genomes of eukaryal viruses of the families Poxviridae, Pycodnaviridae, and Asfarviridae: the two strands of the 32,301 bp long linear genome are covalently connected forming a continuous polynucleotide chain and 2029 kb long inverted repeats are present at the termini. Very likely it also shares with these viruses mechanisms of initiation of replication and resolution of replicative intermediates.
   
   
2. Hewson, I., J. M. O'Neil, C. A. Heil, G. Bratbak, and W. C. Dennison. 2001. Effects of concentrated viral communities on photosynthesis and community composition of co-occurring benthic microalgae and phytoplankton. Aquat.Microb.Ecol. 25:1-10. abstract: Marine viruses have been shown to affect phytoplankton productivity; however, there are no reports on the effect of viruses on benthic microalgae (microphytobenthos). Hence, this study investigated the effects of elevated concentrations of virus-like particles on the photosynthetic physiology and community composition of benthic microalgae and phytoplankton. Virus populations were collected near the sediment surface and concentrated by tangential flow ultrafiltration, and the concentrate was added to benthic and water column samples that were obtained along a eutrophication gradient in the Brisbane River/Moreton Bay estuary, Australia. Photosynthetic and community responses of benthic microalgae, phytoplankton and bacteria were monitored over 7 d in aquaria and in situ. Benthic microalgal communities responded to viral enrichment in both eutrophic and oligotrophic sediments. In eutrophic sediments, Euglenophytes (Euglena sp.) and bacteria decreased in abundance by 20 to 60 and 26 to 66%, respectively, from seawater controls. In oligotrophic sediments, bacteria decreased in abundance by 30 to 42% from seawater controls but the dinoflagellate Gymnodinium sp. increased in abundance by 270 to 3600% from seawater controls, The increased abundance of Gymnodinium sp. may be related to increased availability of dissolved organic matter released from lysed bacteria. Increased (140 to 190% from seawater controls) initial chlorophyll a fluorescence measured with a pulse-amplitude modulated fluorometer was observed in eutrophic benthic microalgal incubations following virus enrichment, consistent with photosystem II damage. Virus enrichment in oligotrophic water significantly stimulated carbon fixation rates, perhaps due to increased nutrient availability by bacterial lysis. The interpretation of data from virus amendment experiments is difficult due to potential interaction with unidentified bioactive compounds within seawater concentrates. However, these results show that viruses are capable of influencing microbial dynamics in sediments.
   
   
3. Hofer, J. S. and R. Sommaruga. 2001. Seasonal dynamics of viruses in an alpine lake: Importance of filamentous forms. Aquat.Microb.Ecol. 26:1-11. abstract: Viruses are an important component of the planktonic food web in freshwater and marine systems, but most studies have been done in the ocean and in lowland lakes. In this work, the seasonal dynamics and structure of the virioplankton as well as their impact on bacteria during a day/night cycle were studied in an alpine lake located 2417 m above sea level. The abundance of virus-like particles (VLP) was determined at 5 discrete depths (0.5 to 8 m) by direct counts with a TEM in samples collected from May to November 1998 at weekly to bi-weekly intervals. Viruses reached the highest abundances under ice (4.6 X 10⁶ VLP ml-1) with a second maximum in autumn. After ice-break, the VLP abundance decreased to undetectable values (<2 X 10⁴ VLP ml-1) probably because of the negative effect of solar radiation that was negatively correlated with the viral abundance in the upper 2 m of the water column (Spearman rank correlation, rs = -0.773, p < 0.01). The virioplankton was morphologically diverse, consisting of forms commonly found in other aquatic systems, but unlike other studies, we found filamentous VLP (FVLP) 450 to 730 nm long that attained abundances of up to 1.3 X 10⁶ ml-1 and accounted for 7 to 100% of the total viral abundance. These FVLP were found occasionally inside filamentous heterotrophic bacteria (> 10 mum) and their respective abundances were positively correlated (rs = 0.728, p < 0.01). The absence of these conspicuous forms in other aquatic ecosystems suggests that FVLP are well adapted to the harsh environmental conditions or are specific to bacterial hosts found in alpine lakes. Finally, between 5 and 28% of the newly produced bacteria were killed by non-filamentous viruses, which therefore are a modest cause of bacterial mortality in this lake.
   
   
4. Larsen, A., T. Castberg, R. A. Sandaa, C. P. D. Brussaard, J. K. Egge, M. Heldal, A. Paulino, R. Thyrhaug, E. J. van Hannen, and G. Bratbak. 2001. Population dynamics and diversity of phytoplankton, bacteria and viruses in a seawater enclosure. Mar.Ecol.Prog.Ser. 221:47-57. abstract: We now know that the abundance of free viruses in most marine environments is high. There is still, however, a lack of understanding of their occurrence and distribution and of in situ relationships between viral and host communities in natural environments. This may be partly due to methodological limitations. Our main aim was therefore to perform a case study in which a variety of methods were applied in order to give an improved, high-resolution description of the microbial communities in a natural environment, In order to do this we combined light microscopy (LM), transmission electron microscopy (TEM), flow cytometry (FCM), PCR denaturing gradient gel electrophoresis (PCR-DGGE) and pulsed-field gel electrophoresis (PFGE) and studied the diversity and succession of algae, bacteria and viruses in a nutrient enriched seawater enclosure. In the enclosure we experienced a situation where the development of the dominating algal population, which consisted of several flagellate species, was followed by proliferation of several different size-classes of viruses. The total bacterial number decreased markedly during the flagellate bloom but the community composition was maintained and the diversity remained high. Our results indicate a close linkage between various algal, bacterial and viral populations and show that virioplankton do not necessarily terminate algal and bacterial blooms but that they keep the host populations at non-blooming levels.
   
   
5. Prangishvili, D., K. Stedman, and W. Zillig. 2001. Viruses of the extremely therophilic archaeon  Sulfolobus. Trends Microbiol. 9:39-42. abstract: Viruses of Sulfolobus  are highly unusual in their morphology, and genome structure and sequence. Certain characteristics of the replication strategies of these viruses and the virus-host interactions suggest relationships with eukaryal and bacterial viruses. Moreover, studying these viruses led to the discovery of archaeal promoters and has provided tools for the development of the molecular genetics of these organisms. The Sulfolobus viruses contain unique regulatory features and structures that undoubtedly hold surprises for researchers in the future.
   
   
6. Simek, K., M. G. Weinbauer, K. Hornak, J. R. Dolan, J. Nedoma, M. Masin, and R. Amann. 2001. Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir. Appl.Environ.Microbiol. 67:2723-2733. abstract: Bacterioplankton from a meso-eutrophic dam reservoir was size fractionated to reduce (<0.8-mum treatment) or enhance (<5-mum treatment) protistan grazing and then incubated in situ for 96 h in dialysis bags. Time course samples were taken from the bags and the reservoir to estimate bacterial abundance, mean cell volume, production, protistan grazing, viral abundance, and frequency of visibly infected cells. Shifts in bacterial community composition (BCC) were examined by denaturing gradient gel electrophoresis (DGGE), cloning and sequencing of 16S rDNA genes from the different treatments, and fluorescence in situ hybridization (PISH) with previously employed and newly designed oligonucleotide probes, Changes in bacterioplankton characteristics were clearly linked to changes in mortality rates. In the reservoir, where bacterial production about equaled protist grazing and viral mortality, community characteristics were nearly invariant, In the "grazer-free" (0.8-mum-filtered) treatment, subject only to a relatively low mortality rate (similar to 17% day(-1)) from viral lysis, bacteria increased markedly in concentration. While the mean bacterial cell volume was invariant, DGGE indicated a shift in BCC and FISH revealed an increase in the proportion of one lineage within the beta proteobacteria, In the grazing-enhanced treatment (5-mum filtrate), grazing mortality was similar to 200% and viral lysis resulted in mortality of 30% of daily production. Cell concentrations declined, and grazing-resistant flocs and filaments eventually dominated the biomass, together accounting for > 80% of the total bacteria by the end of the experiment. Once again, BCC changed strongly and a significant fraction of the large filaments was detected using a FISH probe targeted to members of the Flectobacillus lineage, Shifts of BCC were also reflected in DGGE patterns and in the increases in the relative importance of both beta proteobacteria and members of the Cytophaga-Flavobacterium cluster, which consistently formed different parts of the bacterial flocs. Viral concentrations and frequencies of infected cells were highly significantly correlated with grazing rates, suggesting that protistan grazing may stimulate viral activity.
   
   
7. Brussaard, C. P. D., D. Marie, and G. Bratbak. 2000. Flow cytometric detection of viruses. Journal of Virological Methods 85:175-182. abstract: Representatives from several different virus families (Baculoviridae, Herpesviridae, Myoviridae, Phycodnaviridae, Picornaviridae, Podoviridae, Retroviridae, and Siphoviridae) were stained using a variety of highly fluorescent nucleic acid specific dyes (SYBR Green I, SYBR Green II, OliGreen, PicoGreen) and examined using a standard flow cytometer equipped with a standard 15 mW argon-ion laser. The highest green fluorescence intensities were obtained using SYBR Green I. DNA viruses with genome sizes between 48.5 and 300 kb could easily be detected. The fluorescence signals of the small genome-sized RNA viruses (7.4–14.5 kb) were found at the limit of detection. No significant linear relationship could be found between genome size and the green fluorescence intensity of the SYBR Green I stained virus preparations. To our knowledge, this is the first report of detecting and discriminating between a wide range of different viruses directly using flow cytometry. This rapid and precise assay represents a new and promising tool in the field of virology.
   
   
8. Diez, B., J. Anton, N. Guixa-Boixereu, C. Pedros-Alio, and F. Rodriguez-Valera. 2000. Pulsed-field gel electrophoresis analysis of virus assemblages present in a hypersaline environment. International Microbiology 3:159-164. abstract: A method for analyzing virus assemblages in aquatic environments was developed and used for studying the highest-salinity ponds (from 13.4 to 35% salinity) from a multi-pond solar saltern in Alicante, Spain. The protocol consisted of a series of concentration and purification steps including tangential flow filtration and ultracentrifugation, followed by the preparation of total viral nucleic acids that were subsequently separated by pulsed-field gel electrophoresis. For every sample analyzed, a characteristic DNA pattern was obtained, whose complexity was related to viral diversity. The comparison of our results with a similar analysis carried out with marine virus assemblages shows that, as expected, the viral diversity corresponding to the analyzed hypersaline environment is considerably lower than that of a marine environment
   
   
9. Jeffrey, W. H., J. P. Kase, and S. W. Wilhelm. 2000. Ultraviolet radiation effects on bacterioplankton and viruses in marine ecosystems, p. 206-236. In S. J. De Mora and et al. (eds.), Effects Of UV Radiation On Marine Ecosystems. Cambridge University Press, Cambridge.
   
   
10. Lukasik, J., T. M. Scott, D. Andryshak, and S. R. Farrah. 2000. Influence of salts on virus adsorption to microporous filters. Appl.Environ.Microbiol. 66:2914-2920. abstract: We investigated the direct and indirect effects of mono-, di-, and trivalent salts (NaCl, MgCl(2), and AlCl(3)) on the adsorption of several viruses (MS2, PRD-1, phiX174, and poliovirus 1) to microporous filters at different pH values. The filters studied included Millipore HA (nitrocellulose), Filterite (fiberglass), Whatman (cellulose), and 1MDS (charged-modified fiber) filters. Each of these filters except the Whatman cellulose filters has been used in virus removal and recovery procedures. The direct effects of added salts were considered to be the effects associated with the presence of the soluble salts. The indirect effects of the added salts were considered to be (i) changes in the pH values of solutions and (ii) the formation of insoluble precipitates that could adsorb viruses and be removed by filtration. When direct effects alone were considered, the salts used in this study promoted virus adsorption, interfered with virus adsorption, or had little or no effect on virus adsorption, depending on the filter, the virus, and the salt. Although we were able to confirm previous reports that the addition of aluminum chloride to water enhances virus adsorption to microporous filters, we found that the enhanced adsorption was associated with indirect effects rather than direct effects. The increase in viral adsorption observed when aluminum chloride was added to water was related to the decrease in the pH of the water. Similar results could be obtained by adding HCl. The increased adsorption of viruses in water at pH 7 following addition of aluminum chloride was probably due to flocculation of aluminum, since removal of flocs by filtration greatly reduced the enhancement observed. The only direct effect of aluminum chloride on virus adsorption that we observed was interference with adsorption to microporous filters. Under conditions under which hydrophobic interactions were minimal, aluminum chloride interfered with virus adsorption to Millipore, Filterite, and 1MDS filters. In most cases, less than 10% of the viruses adsorbed to filters in the presence of a multivalent salt and a compound that interfered with hydrophobic interactions (0.1% Tween 80 or 4 M urea).
    
    
11. Middelboe, M. 2000. Bacterial growth rate and marine virus–host dynamics. Microb.Ecol. 40:114-124. abstract: The dynamics of a marine virus–host system were investigated at different steady state growth rates in chemostat cultures and the data were analyzed using a simple model. The virus–host interactions showed strong dependence on host cell growth rate. The duration of the infection cycle and the virus burst size were found to depend on bacterial growth rate, and the rate of cell lysis and virus production were positively correlated with steady state growth rate in the cultures (r ² > 0.96, p < 0.05). At bacterial growth rates of 0.02 to 0.10 h^-1 in the chemostats the virus burst size increased from 12 Ý 4 to 56 Ý 4, and the latent period decreased from 2.0 to 1.7 h. Resistant clones of the host strain were present in the cultures from the beginning of the experiment and replaced the sensitive host cells following viral lysis in the cultures. Regrowth of resistant cells correlated significantly (r ² = 1.000, p < 0.02) with the lysis rate of sensitive cells, indicating that release of viral lysates stimulated growth of the non-infected, resistant cells. The constructed model was suitable for simulating the observed dynamics of the sensitive host cells, viruses and resistant clones in the cultures. The model was therefore used in an attempt to predict the dynamics of this virus–host interaction in a natural marine environment during a certain set of growth conditions. The simulation indicated that a steady state relationship between the specific viruses and sensitive and resistant bacterial clones may occur at densities that are reasonable to assume for natural environments. The study demonstrates that basic characterization and modeling of specific virus–host interactions may improve our understanding of the behavior of bacteria and viruses in natural systems.
    
    
12. Riemann, L., G. F. Steward, and F. Azam. 2000. Dynamics of bacterial community composition and activity during mesocosm diatom blooms. Appl.Environ.Microbiol. 66:578-587. abstract: Bacterial community composition, enzymatic activities, and carbon dynamics were examined during diatom blooms in four, 200 liter laboratory seawater mesocosms.  The objective was to determine whether the dramatic shifts in growth rates and ectoenzyme activities, which are commonly observed during the course of phytoplankton blooms and their subsequent demise, could result from shifts in bacterial community composition.  Nutrient enrichment of metazoan-free seawater resulted in diatom blooms dominated by Thalassiosira sp. which peaked nine days after enrichment ( 24 g chl a l^-1). At this time bacterial abundance abruptly decreased from 2.8 to 0.75 x 10⁶ ml^-1 and analysis of bacterial community composition, by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified, 16S rRNA gene fragments, revealed a disappearance of three dominant phylotypes.  Increased viral and flagellate abundance suggested that both lysis and grazing could have played a role in the observed phylotype-specific mortality.  Subsequently, new phylotypes appeared and bacterial production, abundance and enzyme activities shifted from being predominantly associated with the <1.0 m size-fraction towards the >1.0 m size-fraction indicating a pronounced microbial colonization of particles.  Sequencing of DGGE bands suggested that the observed rapid and extensive colonization of particulate matter was mainly by specialized ??Proteobacteria and Cytophagales-related phylotypes.  These particle-associated bacteria had high growth rates as well as high cell specific aminopeptidase, ??glucosidase and lipase activities.  Rate measurements as well as bacterial population dynamics were almost identical among the mesocosms indicating that the observed bacterial community dynamics were systematic and repeatable responses to the manipulated conditions.
    
    
13. Rodriguez, F., E. Frenandez, R. N. Head, D. S. Harbour, G. Bratbak, M. Heldal, and R. P. Harris. 2000. Temporal variability of viruses, bacteria, phytoplankton and zooplankton in the western English Channel off Plymouth. Journal of the Marine Biological Association of the United Kingdom 80:575-586. abstract: The temporal distribution of autotrophic and heterotrophic components of the planktonic community was studied from samples collected weekly at station L4, located to the south of Plymouth, UK, from October 1992 to January 1994. Phytoplankton succession followed the typical pattern of temperate waters. the development of a summer Gyrodinium aureolum bloom being the most prominent feature. Bacterial numbers were significantly correlated with temperature during autumn and winter, whereas resource availability and predation, including viruses, appear to be the most important controlling factors in spring and summer. High mesozooplankton densities, mainly copepods, were observed throughout most of the study associated with a series of diatom blooms, and also during autumn when low phytoplankton biomass was measured. This data set was analysed in order to build up conceptual trophodynamic models whereby the role of biological communities on the cycling of organic matter could be inferred. The results obtained in this study provide empirical evidence supporting the existence of a succession of trophic organization patterns in a coastal temperate environment. Classical models (herbivorous or microbial webs) appeared episodically whereas transition models (multivorous web) dominated throughout most of the seasonal cycle.
    
    
14. Steward, G. F. and F. Azam. 2000. Analysis of marine viral assemblages, p. 159-165. In C. R. Bell, M. Brylinski, and P. Johnson-Green (eds.), Microbial Biosystems: New Frontiers. Atlantic Canada Society for Microbial Ecology. abstract: Viruses are the numerically dominant microbes in every oceanic environment from the surface into the sediments. A liter of surface seawater from a typical mesotrophic area contains 10¹⁰ of them, about ten times more than bacteria. While total counts of viruses are becoming easier to make, we still know very little about the viruses that comprise a given assemblage.  Infectivity assays are extremely useful and still the best way to assay for infectious viruses for any particular host.  However, this approach requires that each potential host organism be cultured, making it impractical if not impossible to completely characterize natural assemblages.  Morphological studies have been enlightening, but are time consuming and difficult to do quantitatively.  Here we report a fingerprinting approach to characterize natural viral assemblages.  In this approach, viruses are concentrated and intact viral genomes are separated based on their size via pulsed-field gel electrophoresis.  The number of distinguishable bands provides a minimum estimate of the number of different viruses, while band position and staining intensity reveal the genome size distribution within the assemblage.  With this technique we have detected spatial and temporal differences, as well as many similarities, in viral assemblages among a variety of marine habitats. Current efforts are directed toward combining this technique with other methods of fractionation and sequence analysis to allow both morphological and genetic description of uncultivated marine viruses.  Direct investigation of dominant or particularly widespread viruses may ultimately provide clues as to which marine organisms contribute most to the viral pool, and which organisms are likely to be significantly influenced by viral mortality.
    
    
15. Suttle, C. A. 2000. The ecology, evolutionary and geochemical consequences of viral infection of cyanobacteria and eukaryotic algae, p. 248-286. In C. J. Hurst (ed.), Viral Ecology. Academic Press, New York.
    
    
16. Thingstad, T. F. 2000. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol.Oceanogr. 45:1320-1328. abstract: Mechanisms controlling virus abundance and partitioning of loss of bacterial production between viral lysis and protozoan predation are discussed within the framework of an idealized Lotka-Volterra-type model. This combines nonselective protozoan predation with host-selective viral lysis of bacteria. The analysis leads to a reciprocal relationship between bacterial diversity and viruses, in which coexistence of competing bacterial species is ensured by the presence of viruses that "kill the winner," whereas the differences in substrate affinity between the coexisting bacterial species determine viral abundance. The ability of the model to reproduce published observations, such as an approximate 1:10 ratio between bacterial and viral abundance, and the ability of viral lysis to account for 10-50% of bacterial loss are discussed.
    
    
17. Wilhelm, S. W. and R. E. H. Smith. 2000. Bacterial carbon production in Lake Erie is influenced by viruses and solar radiation. Canadian Journal of Fisheries and Aquatic Sciences 57:317-326. abstract: Bacterial production is an integral recycling mechanism that facilitates carbon flow through aquatic food webs. Factors influencing bacterial activity therefore impact carbon flow. Although ecologists consider grazing and dissolved organic carbon flux to be the major regulators of bacterial activity, we explored two other important pressures. Virus-like particle abundance ranged from 3.7 to 37.9 x 10¹⁰ L-1 in samples collected during August 1997 and July 1998. Bacterial abundance during these periods ranged from 1.8 to 4.6 x 10⁹ L-1. Based on electron microscopic analysis, viruses in Lake Erie would have been responsible for 12.1 to 23.4 % of bacterial mortality and, in quasi-steady state conditions, a comparable loss of bacterial productivity. In the central basin, solar radiation was also demonstrated to regulate bacterial productivity. Ultraviolet radiation (UVR, 295-400 nm) was shown to inhibit bacterial productivity according to a cumulative exposure kinetic model, and biological weighting functions were derived to enable calculation of time- and depth-integrated photoinhibition. The daytime photoinhibitory loss of bacterial carbon production was estimated to be 14 to 30% over the upper 5 m, primarily due to UVR > 320 nm. Viruses and sunlight are therefore of comparable importance as regulators of bacterial activity in this system.
    
    
18. Wommack, K. E. and R. R. Colwell. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol.Mol.Biol.Rev. 64:69-114.
    
    
19. Binder, B. 1999. Reconsidering the relationship between virally induced bacterial mortality and frequency of infected cells. Aquat.Microb.Ecol. 18:207-215. abstract: The relative contribution of viral lysis to overall mortality in aquatic bacterial populations is often estimated as twice the frequency of infected cells (FIC). The `factor-of-two rule' upon which this estimate is based assumes (1) steady-state conditions, (2) that latent period is equivalent to generation time, and (3) that infected cells are not grazed. FIC values for this calculation are themselves derived from measurements of the frequency of visibly infected cells (FVIC) by the use of a simple conversion factor. A steady-state model was developed to more rigorously define the relationships between FIC, FVIC, and the fraction of mortality from viral lysis (FMVL). This model shows that even under the restrictive assumptions listed above, the factor-of-two rule systematically overestimates FMVL for typically reported values of FVIC. The model also shows that although grazing on infected cells further reduces FMVL for a given estimate of FIC, at the same time such grazing increases FIC for a given measurement of FVIC. In combination, these 2 effects minimize the influence of grazing on the calculation of FMVL from FVIC. Overall, the relationship between FMVL and FVIC is well approximated as follows: FMVL epsilon FVIC/[ gamma ln(2) (1 - epsilon - FVIC)], where gamma = the ratio between the latent period and generation time, and \g?\ = the fraction of the latent period during which viral particles are not yet visible. Using typically observed values of FVIC, and assuming that gamma = 1 (per assumption 2, above) and \g?\ = 0.186 (per literature estimates), the model suggests that, on average, viral lysis accounts for approximately 22% (range: 4.5 to 45%) of total bacterial mortality in a range of aquatic environments, corresponding to a mean overestimate of 24% (range: 4 to 44%) by the factor-of-two rule. Perhaps most importantly, the model shows that calculations of FMVL from FIC or FVIC are very sensitive to changes in the relative length of the latent period ( gamma ) and in the assumed proportion of the latent period during which viral particles are not recognizable ( epsilon ). Constraining these 2 factors would greatly improve the reliability of FMVL calculations.
    
    
20. Fuhrman, J. A. 1999. Marine viruses and their biogeochemical and ecological effects. Nature 399:541-548. abstract: Viruses are the most common biological agents in the sea, typically numbering ten billion per litre. They probably infect all organisms, can undergo rapid decay and replenishment, and influence many biogeochemical and ecological processes, including nutrient cycling, system respiration, particle size-distributions and sinking rates, bacterial and algal biodiversity and species distributions, algal bloom control, dimethyl sulphide formation and genetic transfer. Newly developed fluorescence and molecular techniques leave the field poised to make significant advances towards evaluating and quantifying such efforts.
    
    
21. Guixa-Boixareu, N., K. Lysnes, and C. Pedros-Alio. 1999. Viral lysis and bacterivory during a phytoplankton bloom in a coastal water microcosm. Appl.Environ.Microbiol. 65:1949-1958. abstract: The relative importance of viral lysis and bacterivory as causes of bacterial mortality were estimated. A laboratory experiment was carried out to check the kind of control that viruses could exert over the bacterial assemblage in a non-steady-state situation. Virus-like particles (VLP) were determined by using three methods of counting (DAPI [4',6-diamidino-2-phenylindole] staining, YOPRO staining, and transmission electron microscopy). Virus counts increased from the beginning until the end of the experiment. However, different methods produced significantly different results. DAPI-stained VLP yielded the lowest numbers, while YOPRO-stained VLP yielded the highest numbers. Bacteria reached the maximal abundance at 122 h (3 x 10 super(7) bacteria ml super(-1)), after the peak of chlorophyll a (80 mu g liter super(-1)). Phototrophic nanoflagellates followed the same pattern as for chlorophyll a. Heterotrophic nanoflagellates showed oscillations in abundance throughout the experiment. The specific bacterial growth rate increased until 168 h (2.6 day super(-1)). The bacterivory rate reached the maximal value at 96 hours (0.9 day super(-1)). Bacterial mortality due to viral infection was measured by using two approaches: measuring the percentage of visibly infected bacteria (%VIB) and measuring the viral decay rates (VDR), which were estimated with cyanide. The %VIB was always lower than 1% during the experiment. VDR were used to estimate viral production. Viral production increased 1 order of magnitude during the experiment (from 10 super(6) to 10 super(7) VLP ml super(-1) h super(-1)). The percentage of heterotrophic bacterial production consumed by bacterivores was higher than 60% during the first 4 days of the experiment; afterwards, this percentage was lower than 10%. The percentage of heterotrophic bacterial production lysed by viruses as assessed by the VDR reached the highest values at the beginning (100%) and at the end (50%) of the experiment. Comparing both sources of mortality at each stage of the bloom, bacterivory was found to be higher than viral lysis at days 2 and 4, and viral lysis was higher than bacterivory at days 7 and 9. A balance between bacterial losses and bacterial production was calculated for each sampling interval. At intervals of 0 to 2 and 2 to 4 days, viral lysis and bacterivory accounted for all the bacterial losses. At intervals of 4 to 7 and 7 to 9 days, bacterial losses were not balanced by the sources of mortality measured. At these time points, bacterial abundance was about 20 times higher than the expected value if viral lysis and bacterivory had been the only factors causing bacterial mortality. In conclusion, mortality caused by viruses can be more important than bacterivory under non-steady-state conditions.
    
    
22. Marie, D., C. P. D. Brussaard, G. Thyrhaug, G. Bratbak, and D. Vaulot. 1999. Enumeration of marine viruses in culture and natural samples by flow cytometry. Appl.Environ.Microbiol. 65:45-52. abstract: Flow cytometry (FCM) was successfully used to enumerate viruses in seawater after staining with the nucleic acid-specific dye SYBR Green-I. The technique was first optimized by using the Phaeocystis lytic virus PpV-01. Then it was used to analyze natural samples from different oceanic locations. Virus samples were fixed with 0.5% glutaraldehyde and deep frozen for delayed analysis. The samples were then diluted in Tris-EDTA buffer and analyzed in the presence of SYBR Green-I. A duplicate sample was heated at 80 degree C in the presence of detergent before analysis. Virus counts obtained by FCM were highly correlated to, although slightly higher than, those obtained by epifluorescence microscopy or by transmission electron microscopy (r = 0.937, n = 14, and r = 0.96, n = 8, respectively). Analysis of a depth profile from the Mediterranean Sea revealed that the abundance of viruses displayed the same vertical trend as that of planktonic cells. FCM permits us to distinguish between at least two and sometimes three virus populations in natural samples. Because of its speed and accuracy, FCM should prove very useful for studies of virus infection in cultures and should allow us to better understand the structure and dynamics of virus populations in natural waters.
    
    
23. Noble, R. T., M. Middelboe, and J. A. Fuhrman. 1999. The effects of viral enrichment on the mortality and growth of heterotrophic bacterioplankton. Aquat.Microb.Ecol. 18:1-13. abstract: The direct effects of viral enrichments upon natural populations of marine viruses and bacteria were studied in seawater from Santa Monica Bay, CA, USA. Active virus concentrates, or control additions (ultrafiltered seawater or autoclaved virus concentrate) were added to 2 l incubations of protist-free seawater, and the effects were monitored for about 3 d. At the beginning of the experiments, the virus numbers reflected the expected addition of intact virus particles as determined by transmission electron microscopy (TEM). Subsequently, the mean frequency of visibly infected bacteria (FVIB; % bacteria which were visibly infected with 5 or more virus-like particles) was greater in the enriched incubations than in the controls. In controls, the estimated percent of bacteria that were infected remained constant at about 5 to 10% of the total bacterial population, but with active enrichment, 10 to 35% of the total bacterial population was infected at a given time. Therefore, by increasing the concentration of active viruses in seawater incubations we were able to increase the amount of bacterial mortality attributed to virus infection. Even with the presumed increase in bacterial mortality, the net increases in bacterial abundance in the samples that were enriched with active virus concentrate were higher than those seen in the controls. The viral abundance in bottles that were enriched with the active virus concentrate was significantly higher than that in the controls in Expts 2 and 3 (p < 0.05), but by the end of the experiments, viral abundances in the enriched incubations approached control levels. In Expts 1 and 2, rates of DOP hydrolysis were higher in the samples enriched with the active virus concentrate, and may have been due to an increase in the incidence of viral lysis. However, overall analysis of DCAA, DFAA, and DOP hydrolysis were quite variable and difficult to interpret. Results indicate that viral enrichment increased the incidence of bacterial infection and consequently stimulated the growth of subpopulations of non-infected heterotrophic bacterioplankton.
    
    
24. Paul, J. H. 1999. Microbial gene transfer: an ecological perspective. J.Mol.Microbiol.Biotechnol. 1:45-50. abstract: Microbial gene transfer or microbial sex is a means of exchanging loci amongst prokaryotes and certain eukaryotes. Historically viewed as a laboratory artifact, recent evidence from natural populations as well as genome research has indicated that this process may be a major driving force in microbial evolution. Studies with natural populations have taken two approaches-either adding a defined donor with a traceable gene to an indigenous community, and detecting the target gene in the indigenous bacteria, or by adding a model recipient to capture genes being transferred from the ambient microbial flora. However, both approaches usually require some cultivation of the recipient, which may result in a dramatic underestimation of the ambient transfer frequency. Novel methods are just evolving to study  in situ gene transfer processes, including the use of green fluorescent protein (GFP)-marked plasmids, which enable detection of transferrants by epifluorescence microscopy. A transduction-like mechanism of transfer from viral-like particles produced by marine bacteria and thermal spring bacteria to Escherichia coli has been documented recently, indicating that broad host range transduction may be occurring in aquatic environments. The sequencing of complete microbial genomes has shown that they are a mosaic of ancestral chromosomal genes interspersed with recently transferred operons that encode peripheral functions. Archaeal genomes indicate that the genes for replication, transcription, and translation are all eukaryotic in complexity, while the genes for intermediary metabolism are purely bacterial. And in eukaryotes, many ancestral eukaryotic genes have been replaced by bacterial genes believed derived from food sources. Collectively these results indicate that microbial sex can result in the dispersal of loci in contemporary microbial populations as well as having shaped the phylogenies of microbes from multiple, very early gene transfer events.
    
    
25. Prangishvili, D., H. P. Arnold, D. Gotz, U. Ziese, I. Holz, J. K. Kristjansson, and W. Zillig. 1999. A novel virus family, the Rudiviridae: Structure, virus-host interactions and genome variability of the sulfolobus viruses SIRV1 and SIRV2. Genetics 152:1387-1396. abstract: The unenveloped, stiff-rod-shaped, linear double-stranded DNA viruses SIRV1 and SIRV2 from Icelandic Sulfolobus isolates form a novel virus family, the Rudiviridae. The sizes of the genomes are 32. 3 kbp for SIRV1 and 35.8 kbp for SIRV2. The virions consist of a tube-like superhelix formed by the DNA and a single basic 15.8-kD DNA-binding protein. The tube carries a plug and three tail fibers at each end. One turn of the DNA-protein superhelix measures 4.3 nm and comprises 16.5 turns of B DNA. The linear DNA molecules appear to have covalently closed hairpin ends. The viruses are not lytic and are present in their original hosts in carrier states. Both viruses are quite stable in these carrier states. In several laboratory hosts SIRV2 was invariant, but SIRV1 formed many different variants that completely replaced the wild-type virus. Some of these variants were still variable, whereas others were stable. Up to 10% nucleotide substitution was found between corresponding genome fragments of three variants. Some variants showed deletions. Wild-type SIRV1, but not SIRV2, induces an SOS-like response in Sulfolobus. We propose that wild-type SIRV1 is unable to propagate in some hosts but surmounts this host range barrier by inducing a host response effecting extensive variation of the viral genome.
    
    
26. Short, S. M. and C. A. Suttle. 1999. Use of the polymerase chain reaction and denaturing gradient gel electrophoresis to study diversity in natural virus communities. Hydrobiologia 401:19-32. abstract: Viruses are abundant members of marine and freshwater microbial communities, and are important players in aquatic ecology and geochemical cycles. Recent methodological developments have allowed the use of the polymerase chain reaction (PCR) to examine the diversity of natural communities of viruses without the need for culture. DNA polymerase genes are highly conserved and are, therefore, suitable targets for PCR analysis of microbes that do not encode rRNA. As natural virus communities are largely made up of dsDNA viruses, and as many dsDNA algal viruses encode their own DNA polymerase, PCR primers can be designed to amplify fragments of these genes. This approach has been used to examine the genetic diversity in natural communities of viruses that infect phytoplankton. Algal-virus-specific primers were used to amplify polymerase fragments from natural virus samples, demonstrating the presence of a diverse community of viruses closely related to those that are known to infect phytoplankton. We have modified this approach by using denaturing gradient gel electrophoresis (DGGE) to rapidly analyze PCR products. DGGE will permit rapid and efficient fingerprinting of natural marine viral communities, and allow spatial and temporal differences in viral community structure to be examined. This paper provides a brief overview of how PCR and DGGE can be used to examine diversity in natural viral communities drawing on viruses that infect phytoplankton as an example.
    
    
27. Sommaruga, R., B. Sattller, A. Oberleiter, A. Wille, S. Sommaruga-Wögrath, R. Psenner, M. Felip, L. Camarero, S. Pina, R. GironTs, and J. Catalán. 1999. An in situ enclosure experiment to test the solar UVB impact on plankton in a high altitude mountain lake: II) effects on the microbial food web. Journal of Plankton Research 21:859-879. abstract: We studied the impact of ambient levels of solar UVB radiation on the planktonic microbial food web (viruses, heterotrophic bacteria, heterotrophic flagellates and ciliates) of a high-mountain lake (2417 m above sea level) under in situ conditions for 16 days. Enclosures of 1 m3 receiving either the full sunlight spectrum or sunlight without UVB radiation were suspended at the lake surface.  We found that the abundance of heterotrophic flagellates was always lower in the +UVB treatment than in the -UVB one. In addition, bacterial consumption, measured by the disappearance of fluorescently labelled bacteria, was significantly (p<0.05) reduced in the +UVB treatment. The abundance of non-filamentous bacteria (<10 Ým long) was also lower in the +UVB treatment, suggesting a direct effect of UVB on their growth. This was supported by the significantly (p<0.05) lower cell-specific activity ([3H]-thymidine incorporation) found on the fifth day of the experiment. In contrast, UVB radiation had no effect on filamentous bacteria (>10 Ým long) that represented only a small fraction of the total abundance (<4%) but up to ~70 % of the total bacterial biovolume. Ciliates, mainly Urotricha pelagica and U. furcata, were less impacted by UVB radiation although the net growth rate during the first week of the experiment was lower in the +UVB treatment than in the -UVB one (0.22 and 0.39 d-1, respectively). The abundance of virus-like particles during the first week of the experiment was higher in the -UVB treatment. After reaching the maximum value for the interaction viruses x bacteria, their number decreased dramatically (by ~85%) in both treatments with a decay rate of ~0.017 h-1. This study illustrates the complexity in assessing the impact of UVB radiation when more than one trophic level is considered and indicates the existence of different sensitivity to UVB radiation among components of the microbial food web.
    
    
28. van Hannen, E. J., G. Zwart, M. P. van Agterveld, H. J. Gons, J. Ebert, and H. J. Laanbroek. 1999. Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Appl.Environ.Microbiol. 65:795-801. abstract: During an experiment in two laboratory-scale enclosures filled with lake water (130 liters each) we noticed the almost-complete lysis of the cyanobacterial population. Based on electron microscopic observations of viral particles inside cyanobacterial filaments and counts of virus-like particles, we concluded that a viral lysis of the filamentous cyanobacteria had taken place. Denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA fragments qualitatively monitored the removal of the cyanobacterial species from the community and the appearance of newly emerging bacterial species. The majority of these bacteria were related to the Cytophagales and actinomycetes, bacterial divisions known to contain species capable of degrading complex organic molecules. A few days after the cyanobacteria started to lyse, a rotifer species became dominant in the DGGE profile of the eukaryotic community. Since rotifers play an important role in the carbon transfer between the microbial loop and higher trophic levels, these observations confirm the role of viruses in channeling carbon through food webs. Multidimensional scaling analysis of the DGGE profiles showed large changes in the structures of both the bacterial and eukaryotic communities at the time of lysis. These changes were remarkably similar in the two enclosures, indicating that such community structure changes are not random but occur according to a fixed pattern. Our findings strongly support the idea that viruses can structure microbial communities.
    
    
29. Wilhelm, S. W. and C. A. Suttle. 1999. Viruses and nutrient cycles in the sea. BioScience 49:781-788. abstract: Viruses play critical roles in the structure and function of aquatic food webs.
    
    
30. Wommack, K. E., J. Ravel, R. T. Hill, and R. R. Colwell. 1999. Population dynamics of Chesapeake Bay virioplankton: total-community analysis by pulsed-field gel electrophoresis. Appl.Environ.Microbiol. 65:231-240. abstract: It has been hypothesized that, by specifically lysing numerically dominant host strains, the virioplankton may play a role in maintaining clonal diversity of heterotrophic bacteria and phytoplankton populations. If viruses selectively lyse only those host species that are numerically dominant, then the number of a specific virus within the virioplankton would be expected to change dramatically over time and space, in coordination with changes in abundance of the host. In this study, the abundances of specific viruses in Chesapeake Bay water samples were monitored, using nucleic acid probes and hybridization analysis. Total virioplankton in a water sample was separated by pulsed-field gel electrophoresis and hybridized with nucleic acid probes specific to either single viral strains or a group of viruses with similar genome sizes. The abundances of specific viruses were inferred from the intensity of the hybridization signal. By using this technique, a virus comprising 1/1,000 of the total virioplankton abundance (ca. 10(4) PFU/ml) could be detected. Titers of either a single virus species or a group of viruses changed over time, increasing to peak abundance and then declining to low or undetectable levels, and were geographically localized in the bay. Peak signal intensities, i.e., peak abundances of virus strains, were 10-fold greater than the low background level. Furthermore, virus species were found to be restricted to a particular depth, since probes specific to viruses from bottom water did not hybridize with virus genomes from surface water at the same geographical location. Overall, changes in abundances of specific viruses within the virioplankton were episodic, supporting the hypothesis that viral infection influences, if not controls, clonal diversity within heterotrophic bacteria and phytoplankton communities.
    
    
31. Wommack, K. E., J. Ravel, R. T. Hill, and R. R. Colwell. 1999. Hybridization analysis of Chesapeake Bay Virioplankton. Appl.Environ.Microbiol. 65:241-250. abstract: It has been hypothesized that, by specifically lysing numerically dominant host strains, the virioplankton may play a role in maintaining clonal diversity of heterotrophic bacteria and phytoplankton populations. If viruses selectively lyse only those host species that are numerically dominant, then the number of a specific virus within the virioplankton would be expected to change dramatically over time and space, in coordination with changes in abundance of the host. In this study, the abundances of specific viruses in Chesapeake Bay water samples were monitored, using nucleic acid probes and hybridization analysis. Total virioplankton in a water sample was separated by pulsed-field gel electrophoresis and hybridized with nucleic acid probes specific to either single viral strains or a group of viruses with similar genome sizes. The abundances of specific viruses were inferred from the intensity of the hybridization signal. By using this technique, a virus comprising 1/1,000 of the total virioplankton abundance (ca. 10(4) PFU/ml) could be detected. Titers of either a single virus species or a group of viruses changed over time, increasing to peak abundance and then declining to low or undetectable levels, and were geographically localized in the bay. Peak signal intensities, i.e., peak abundances of virus strains, were 10-fold greater than the low background level. Furthermore, virus species were found to be restricted to a particular depth, since probes specific to viruses from bottom water did not hybridize with virus genomes from surface water at the same geographical location. Overall, changes in abundances of specific viruses within the virioplankton were episodic, supporting the hypothesis that viral infection influences, if not controls, clonal diversity within heterotrophic bacteria and phytoplankton communities.  
    
    
32. Bath, C. and M. L. Dyall-Smith . 1998. His1, and archaeal virus of the Fuselloviridae  family that infects Haloarcula hispanica. J.Virol. 72:9392-9395. abstract: A novel archaeal virus, His1, was isolated from hypersaline waters in south-eastern Australia.  It was lytic, grew only on Ha. hispanica (up to titres of 1011p.f.u./ml), and displayed a "lemon-shaped" morphology (74nm x 44nm) previously reported only for a virus of the extreme thermophiles (SSV1).  The density of His1 was approximately 1.28g/ml - similar to that of SSV1 (1.24g/ml).  Purified particles were resistant to low salt.  The genome was linear, dsDNA and 14.9kb in size, which was similar in size to the genome of the SSV1 (ie. 15.5kb).  Morphologically, this isolate clearly belongs to the recently proposed Fuselloviridae family of archaeal viruses.  It represents the first member from the extremely halophilic archaea, and its host, Ha. hispanica, is one that can be readily manipulated genetically.
    
    
33. Clarke, K. J. 1998. Virus particle production in lysogenic bacteria exposed to protozoan grazing. FEMS Microbiol.Let. 166:177-180. abstract: Electron microscopy was used to investigate the apparent induction of virus particle production in bacteria undergoing digestion by ciliates. Results showed that numbers of bacteria containing virus particles increased by a factor of 25 when enclosed within ciliate food vacuoles. It was also found that 10% of these particles survived the digestion process to be released back into the aquatic habitat within faecal pellets. The possibility of virus gene transfer occurring between lysogenically infected bacteria that survive the ciliate digestive processes, is also considered.
    
    
34. Juniper, S. K., D. F. Bird, M. Summit, M. Pong Vong, and E. T. Baker. 1998. Bacterial and viral abundances in hydrothermal event plumes over northern Gorda Ridge. Deep-Sea Research 45:2739-2749. abstract: This study presents first-time observations of bacterial and viral abundances in hydrothermal event plumes. Two water-column event plumes were formed in conjunction with seismic events and seafloor volcanic eruptions on the northern Gorda Ridge in February--March 1996. Epifluorescence counts of bacteria and viruses were performed on water samples from 3 successive cruises staged in the 10--90 days that followed the onset of seismicity. Relative to background seawater at these 1800--3200 m depths, bacterial abundance was enhanced by 2-3 fold within both event plumes. In contrast, viral numbers were below background seawater values in the younger and more intense of the two event plumes (EP96A), and enhanced in the other (EP96B). Changes in viral abundance may be a secondary response to that of plume bacteria as well as being influenced by particle formation and precipitation within the plumes. Lower bacteria/heat, virus/heat and virus/bacteria ratios in EP96A versus EP96B confirm distinct differences in the microbial response to event plume formation, possibly related to observed differences in plume chemistry.
    
    
35. Noble, R. T. and J. A. Fuhrman . 1998. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat.Microb.Ecol. 14:113-118. abstract: A new nucleic acid stain, SYBR Green I, can be used for the rapid and accurate determination of viral and bacterial abundances in diverse marine samples. We tested this stain with formalin-preserved samples of coastal water and also from depth profiles (to 800 m) from sites 19 and 190 km offshore, by filtering a few ml onto 0.02 mu m pore-size filters and staining for 15 min. Comparison of bacterial counts to those made with acridine orange (AO) and virus counts with those made by transmission electron microscopy (TEM) showed very strong correlations. Bacterial counts with AO and SYBR Green I were indistinguishable and almost perfectly correlated (r super(2) = 0.99). Virus counts ranged widely, from 0.03 to 15 x 10 super(7) virus ml super(-1). Virus counts by SYBR Green I were on the average higher than those made by TEM, and a SYBR Green I versus TEM plot yielded a regression slope of 1.28. The correlation between the two was very high with an r super(2) value of 0.98. The precision of the SYBR Green I method was the same as that for TEM, with coefficients of variation of 2.9%. SYBR Green I stained viruses and bacteria are intensely stained and easy to distinguish from other particles with both older and newer generation epifluorescence microscopes. Detritus is generally not stained, unlike when the alternative dye YoPro I is used, so this approach may be suitable for sediments. SYBR Green I stained samples need no desalting or heating, can be fixed with formalin prior to filtration, the optimal staining time is 15 min (resulting in a total preparation time of less than 25 min), and counts can be easily performed at sea immediately after sampling. This method may facilitate incorporation of viral research into most aquatic microbiology laboratories.
    
    
36. Pina, S., A. Creus, N. Ganzález, R. GironTs, M. Felip, and R. Sommaruga. 1998. Abundance, morphology and distribution of planktonic virus-like particles in two high-mountain lakes. Journal of Plankton Research 20:2413-2421. abstract: Direct counts of virus-like particles (VLP) by transmission electron microscopy revealed abundances of up to 3 x 10⁷ ml^-1 in the plankton of two remote high-mountain lakes in the Alps and in the Pyrenees. Most VLP were icosahedric without tail and with diameters between 40 and 90 nm, but also very large ones with diameter of up to 325 nm were observed. VLP outnumbered bacteria by a factor of 4.2 to 42.8 and bacterial cells were infected with large numbers (>50) of viral particles. This study constitutes the first report on aquatic viruses for alpine lakes and it suggests that they may be an important additional source of bacterial mortality in these systems.
    
    
37. Prangishvili, D., H. P. Klenk, G. Jakobs, A. Schmiechen, C. Hanselmann, I. Holz, and W. Zillig. 1998. Biochemical and phylogenetic characterization of the dUTPase from the archaeal virus SIRV. Journal of Biological Chemistry 273:6024-6029. abstract: The derived amino acid sequence from a 474-base pair open reading frame in the genome of the Sulfolobus islandicus rod-shaped virus SIRV shows striking similarity to bacterial dCTP deaminases and to dUTPases from eukaryotes, bacteria, Poxviridae, and Retroviridae. The putative gene was expressed in Escherichia coli, and dUTPase activity of the recombinant enzyme was demonstrated by hydrolysis of dUTP to dUMP. Deamination of dCTP by the enzyme was not detected. Phylogenetic analysis based on amino acid sequences of the characterized enzyme and its homologues showed that the dUTPase-encoding dut genes and the dCTP deaminase-encoding dcd genes constitute a paralogous gene family. This report is the first identification and functional characterization of an archaeal dUTPase and the first phylogeny derived for the dcd-dut gene family.
    
    
38. Thingstad, T. F. 1998. A theoretical approach to structuring mechanisms in the pelagic food web. Hydrobioligia 363:59-72. abstract: In the literature there is a commonly used idealized concept of the food web structure in the pelagic photic zone food web, based to a large extent on size dependent relationships. An outline is here given of how the elementary size-related physical laws of diffusion and sinking, combined with the assumption of predators being size selective in their choice of prey, give a theoretical foundation for this type of structure. It is shown how such a theoretical fundament makes it possible to relate a broad specter of phenomena within one generic and consistent framework. Phenomena such as Hutchinson's and Goldman's paradoxes, the influence of nutrients and water column stability on the balance between microbial and classical food webs, bacterial carbon consumption, new production and export of DOC and POC to the aphotic zone, eutrophication and diversity, can all be approached from this perspective. By including host-specific viruses, this approach gives a hierarchical structure to the control of diversity with nutrient content controlling the maximum size of the photic zone community, size selectivity of predators regulating how the nutrient is distributed between size-groups of osmotrophic and phagotrophic organisms, and viral host specificity regulating how the nutrients within a size group is distributed between host groups. I also briefly discuss how some biological strategies may be successful by not conforming to the normal rules of such a framework. Analyzing the behavior of these idealized systems is thus claimed to facilitate our understanding of the behavior of complex natural food webs.
    
    
39. Weinbauer, M. G. and M. G. Hoefle. 1998. Size-specific mortality of lake bacterioplankton by natural virus communities. Aquat.Microb.Ecol. 15:103-113. abstract: The potential effect that viral lysis has on the cell size distribution of bacterioplankton was investigated during late summer stratification in Lake Plusssee, Germany. Size-specific bacterial mortality due to viral lysis was estimated from in situ samples by a transmission electron microscopy based examination of visibly infected cells (VIC) and in an experiment with varying concentrations of the natural virus community. In all depth layers the highest percentage of cells was found in a cell length class that was smaller for the entire bacterial community (0.3-0.6 mu m) than for VIC (0.6-0.9 mu m). For cells <2.4 mu m the highest frequency of VIC (FVIC) was detected in the size classes 0.6-0.9 and 0.9-1.2 mu m, and the FVIC was high in the size classes 1.2-1.5 (all depth layers) and 1.5-1.8 mu m (meta- and hypolimnion). The estimated mortality due to viral lysis in these size classes was significant with maxima of 29 to 55% in the epilimnion, 30 to 59% in the metalimnion and 56 to 107% in the hypolimnion. In all depth layers the FVIC of bacteria <0.3 mu m in length was ca 30% of that averaged for the entire bacterial community, and in the experiment the percentage of cells <0.3 mu m was highest in enclosures with high viral activity.
    
    
40. Weinbauer, M. G. and M. G. Höfle. 1998. Cell size-specific lysis of lake bacterioplankton by natural virus communities. Aquat.Microb.Ecol. 156:103-113. abstract: The potential effect that viral lysis has on the cell size distribution of bacterioplankton was investigated during late summer stratification in Lake Plusssee, Germany. Size-specific bacterial mortality due to viral lysis was estimated from in situ samples by a transmission electron microscopy based examination of visibly infected cells (VIC) and in an experiment with varying concentrations of the natural virus community. In all depth layers the highest percentage of cells was found in a cell length class that was smaller for the entire bacterial community (0.3-0.6 mu m) than for VIC (0.6-0.9 mu m). For cells <2.4 mu m the highest frequency of VIC (FVIC) was detected in the size classes 0.6-0.9 and 0.9-1.2 mu m and the FVIC was high in the size classes 1.2-1.5 (all depth layers) and 1.5-1.8 mu m (meta- and hypolimnion). The estimated mortality due to viral lysis in these size classes was significant with maxima of 29 to 55% in the epilimnion, 30 to 59% in the metalimnion and 56 to 107% in the hypolimnion. In all depth layers the FVIC of bacteria <0.3 mu m in length was ca 30% of that averaged for the entire bacterial community, and in the experiment the percentage of cells <0.3 mu m was highest in enclosures with high viral activity. In the experiment the average cell size was smaller in enclosures with high than in that with low viral activity. The data demonstrate that being small could be a strategy of cells to reduce mortality due to viral lysis probably by reducing the contact rates with viruses. Thus, viral lysis could be one of the mechanisms keeping the cell size small in aquatic ecosystems. In oxic water cells in the largest size class (>2.4 mu m) were not infected with viruses, and in enclosures with epilimnetic lake water the percentage of cells >2.4 mu m was highest in enclosures with highest viral abundance, suggesting that resistance against infection favored large cells. However, in the meta- and hypolimnion the FVIC was high for cells >2.4 mu m and, since the burst size increased with bacterial cell size, lysis of large cells could contribute significantly to viral production. Also, a major portion of biomass was found in cells >2.4 mu m. The finding that viral lysis is size-specific and can affect the cell size distribution of bacteria in lake water has important implications for our understanding of the mechanisms which regulate bacterial production and nutrient cycling in pelagic environments.
    
    
41. Weinbauer, M. G. and M. G. Hofle. 1998. Significance of viral lysis and flagellate grazing as factors controlling bacterioplankton production in a eutrophic lake. Appl.Environ.Microbiol. 64:431-438. abstract: The effects of viral lysis and heterotrophic nanoflagellate (HNF) grazing on bacterial mortality were estimated in a eutrophic lake (Lake Plussee in northern Germany) which was separated by a steep temperature and oxygen gradient into a warm and oxic epilimnion and a cold and anoxic hypolimnion. Two transmission electron microscopy-based methods (whole-cell examination and thin sections) were used to determine the frequency of visibly infected cells, and a model was used to estimate bacterial mortality due to viral lysis. Examination of thin sections also showed that between 20.2 and 29.2% (average, 26.1%) of the bacterial cells were empty (ghosts) and thus could not contribute to viral production. The most important finding was that the mechanism for regulating bacterial production shifted with depth from grazing control in the epilimnion to control due to viral lysis in the hypolimnion. We estimated that in the epilimnion viral lysis accounted on average for 8.4 to 41.8% of the summed mortality (calculated by determining the sum of the mortalities due to lysis and grazing), compared to 51.3 to 91.0% of the summed mortality in the metalimninon and 88.5 to 94.2% of the summed mortality in the hypolimnion. Estimates of summed mortality values indicated that bacterial production was controlled completely or almost completely in the epilimnion (summed mortality, 66.6 to 128.5%) and the hypolimnion (summed mortality, 43.4 to 103.3%), whereas in the metalimnion viral lysis and HNF grazing were not sufficient to control bacterial production (summed mortality, 22.4 to 56.7%). The estimated contribution of organic matter released by viral lysis of cells into the pool of dissolved organic matter (DOM) was low; however, since cell lysis products are very likely labile compared to the bulk DOM, they might stimulate bacterial production. The high mortality of bacterioplankton due to viral lysis in anoxic water indicates that a significant portion of bacterial production in the metalimnion and hypolimnion is cycled in the bacterium-virus-DOM loop. This finding has major implications for the fate and cycling of organic nutrients in lakes.
    
    
42. Wilhelm, S. W., M. G. Weinbauer, C. A. Suttle, and W. H. Jeffrey. 1998. The role of sunlight in the removal and repair of viruses in the sea. Limnol.Oceanogr. 43:586-592. abstract: We investigated the in situ destruction rates of marine viral particles as well as the decay rates of infectivity for viral isolates along an similar to 400-km transect from oligotrophic offshore waters to productive coastal waters in the Gulf of Mexico. Light-mediated decay rates of viral infectivity averaged over the solar day ranged from 0.7 to 0.85 h super(-1) in surface waters at all stations and decreased with depth in proportion to the attenuation of UVB (305 nm). The destruction rates of viral particles also decreased with depth, although the rates of particle destruction were only 22-61% of infectivity when integrated over the mixed layer. The rates of viral particle destruction indicated that at three of four stations 6-12% of the daily bacterial production would have to be lysed in order to maintain ambient viral concentrations. At the fourth station, where there was a dense bloom of Synechococcus spp. and the mixed layer was shallower, 34-52% of the daily bacterial production would have to be lysed. A comparison of the difference between destruction rates of viral particles and infectivity integrated over the depth of the mixed layer implies that host-mediated repair must have restored infectivity to 39-78% of the sunlight-damaged viruses daily. The calculated frequency of contacts between viral particles and bacterial cells that resulted in infection (contact success) ranged from similar to 18 to 34% in offshore waters, where the frequency of contacts between viruses and bacteria was much lower, to similar to 1.0% at the most inshore station, where contact rates are much higher. This suggests that in offshore waters bacterial communities are less diverse, and that there is less selection to be resistant to viral infection. This paper provides a framework for balancing viral production, destruction, and light-dependent repair in aquatic viral communities.
    
    
43. Wilhelm, S. W., M. G. Weinbauer, C. A. Suttle, R. J. Pledger, and D. L. Mitchell. 1998. Measurements of DNA damage and photoreactivation imply that most viruses in marine surface waters are inefective. Aquat.Microb.Ecol. 14:215-222. abstract: The proportion of viruses in natural marine communities that are potentially infectious was inferred from the relationship between DNA damage and the loss of infectivity in marine viral isolates and measurements of the DNA damage in natural viral communities. Several viral isolates which infect marine Vibrio spp. were exposed to UV-C radiation and the concentration of cyclobutane pyrimidine dimers in the viral DNA was measured with a highly sensitive radioimmunoassay. The loss of infectivity in the UV-exposed isolates was also determined under conditions which either activated or repressed the blue light dependent photolyase enzyme in host cells in order to examine the damage-dependent response of this bacterial repair system. In addition, the accumulation of DNA photodamage during the solar day was measured in DNA isolated from natural viral communities collected along a transect in the western Gulf of Mexico. Using the correlation between DNA damage and infectivity for one of the viral isolates, we estimated the proportion of the natural viral community which was infective. The results imply that, due to light-mediated repair of damaged viral DNA by host-cell mechanisms (photoreactivation), greater than 50% of the viruses in natural communities are infective despite high rates of DNA damage. Furthermore, the accumulation of cyclobutane pyrimidine dimers was highest at the station where the surface mixed layer was shallowest, emphasizing the importance of mixing depth in relation to the accumulation of DNA damage. These experiments demonstrate that physical parameters such as mixing depth are critically interwoven with light penetration in influencing the infectivity of marine viral communities.
    
    
44. Wilson, W. H., S. Turner, and N. H. Mann. 1998. Population dynamics of phytoplankton and viruses in a phosphate-limited mesocosm and their effect on DMSP and DMS production. Estuarine, Coastal and Shelf Science 46 (Supplement a):49-59. abstract: The effect of phosphate limitation on viral abundance, phytoplankton bloom dynamics and production of dimethylsulphoniopropionate (DMSP) and dimethyl sulphide (DMS) was investigated in seawater mesocosm enclosures, in a Norwegian fjord, during June 1995. Daily estimates of viral concentrations, based on transmission electron microscope (TEM) counts, varied on an apparently random basis in each of the enclosures. A large Synechococcus spp. bloom developed in an enclosure which was maintained at a high N:P ratio, simulating phosphate-deplete growth conditions. Following phosphate addition to this enclosure, there was a large increase in estimated virus numbers shortly before an apparent collapse of the Synechococcus bloom. It is tentatively suggested that lysogenic viruses were induced following phosphate addition to the phosphate-limited enclosures, and that these observations add to a growing body of evidence which supports the hypothesis that nutrient availability may be responsible for the switch between lysogeny and lytic production. High DMS concentrations and viral numbers were observed on the demise of the flagellate (predominantly Emiliania huxleyi) and diatom blooms, but overall there was no significant correlation. Highest concentrations of DMSP were associated with blooms of E. huxleyi, for which an intracellular concentration of 0.5 pg cell-1 (SD, 0.06) was calculated. Good correlation of DMSP with Synechococcus spp. cell numbers was observed, suggesting that these species of picoplankton may be significant producers of DMSP. No effects of phosphate limitation on DMS and/or DMSP production were evident from the data.
    
    
45. Wilhelm, S. W., M. G. Weinbauer, C. A. Suttle, R. J. Pledger, and D. L. Mitchell. 1998. Measurements of DNA damage and photoreactivation imply that most viruses in marine surface waters are inefective. Aquat.Microb.Ecol. 14:215-222. abstract: The proportion of viruses in natural marine communities that are potentially infectious was inferred from the relationship between DNA damage and the loss of infectivity in marine viral isolates and measurements of the DNA damage in natural viral communities. Several viral isolates which infect marine Vibrio spp. were exposed to UV-C radiation and the concentration of cyclobutane pyrimidine dimers in the viral DNA was measured with a highly sensitive radioimmunoassay. The loss of infectivity in the UV-exposed isolates was also determined under conditions which either activated or repressed the blue light dependent photolyase enzyme in host cells in order to examine the damage-dependent response of this bacterial repair system. In addition, the accumulation of DNA photodamage during the solar day was measured in DNA isolated from natural viral communities collected along a transect in the western Gulf of Mexico. Using the correlation between DNA damage and infectivity for one of the viral isolates, we estimated the proportion of the natural viral community which was infective. The results imply that, due to light-mediated repair of damaged viral DNA by host-cell mechanisms (photoreactivation), greater than 50% of the viruses in natural communities are infective despite high rates of DNA damage. Furthermore, the accumulation of cyclobutane pyrimidine dimers was highest at the station where the surface mixed layer was shallowest, emphasizing the importance of mixing depth in relation to the accumulation of DNA damage. These experiments demonstrate that physical parameters such as mixing depth are critically interwoven with light penetration in influencing the infectivity of marine viral communities.