Christian Winter

Trade-Offs between Competition and Defense Specialists among Unicellular Planktonic Organisms: the “Killing the Winner” Hypothesis Revisited

SUMMARY A trade-off between strategies maximizing growth and minimizing losses appears to be a fundamental property of evolving biological entities existing in environments with limited resources. In the special case of unicellular planktonic organisms, the theoretical framework describing the trade-offs between competition and defense specialists is known as the “killing the winner” hypothesis (KtW). KtW describes how the availability of resources and the actions of predators (e.g., heterotrophic flagellates) and parasites (e.g., viruses) determine the composition and biogeochemical impact of such organisms. We extend KtW conceptually by introducing size- or shape-selective grazing of protozoans on prokaryotes into an idealized food web composed of prokaryotes, lytic viruses infecting prokaryotes, and protozoans. This results in a hierarchy analogous to a Russian doll, where KtW principles are at work on a lower level due to selective viral infection and on an upper level due to size- or shape-selective grazing by protozoans. Additionally, we critically discuss predictions and limitations of KtW in light of the recent literature, with particular focus on typically neglected aspects of KtW. Many aspects of KtW have been corroborated by in situ and experimental studies of isolates and natural communities. However, a thorough test of KtW is still hampered by current methodological limitations. In particular, the quantification of nutrient uptake rates of the competing prokaryotic populations and virus population-specific adsorption and decay rates appears to be the most daunting challenge for the years to come.

Impact of Virioplankton on Archaeal and Bacterial Community Richness as Assessed in Seawater Batch Cultures

ABSTRACT During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and Bacteria. One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.

Longitudinal Changes in the Bacterial Community Composition of the Danube River: a Whole-River Approach†

ABSTRACT The Danube River is the second longest river in Europe, and its bacterial community composition has never been studied before over its entire length. In this study, bacterial community composition was determined by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified portions of the bacterial 16S rRNA gene from a total of 98 stations on the Danube River (73 stations) and its major tributaries (25 stations), covering a distance of 2,581 km. Shifts in the bacterial community composition were related to changes in environmental conditions found by comparison with physicochemical parameters (e.g., temperature and concentration of nutrients) and the concentration of chlorophyll a (Chl a). In total, 43 distinct DGGE bands were detected. Sequencing of selected bands revealed that the phylotypes were associated with typical freshwater bacteria. Apparent bacterial richness in the Danube varied between 18 and 32 bands and correlated positively with the concentration of P-PO4 (r = 0.56) and negatively with Chl a (r = −0.52). An artificial neural network-based model explained 90% of the variation of apparent bacterial richness using the concentrations of N-NO2 and P-PO4 and the distance to the Black Sea as input parameters. Between the cities of Budapest and Belgrade, apparent bacterial richness was significantly lower than that of other regions of the river, and Chl a showed a pronounced peak. Generally, the bacterial community composition developed gradually; however, an abrupt and clear shift was detected in the section of the phytoplankton bloom. Large impoundments did not have a discernible effect on the bacterial community of the water column. In conclusion, the riverine bacterial community was largely influenced by intrinsic factors.

Terminal-restriction fragment length polymorphism T-RFLP screening of a marine archaeal clone library to determine the different phylotypes

T-RFLP clone characterization (screening) was optimized for a fast and basepair-accurate characterization of clones from marine Archaea collected from the Eastern Mediterranean Sea. Because of the high sensitivity of T-RFLP fingerprinting, a protocol was developed where 10 initial PCR cycles gave detectable terminal fragments from clones. Additionally, forward and reverse primers for PCR were individually labeled and detected simultaneously to assess the suitability of the forward and reverse fragments for T-RFLP screening. Based on independent restriction digests with the tetrameric restriction enzymes HhaI, RsaI and HaeIII to characterize the 49 archaeal clones in our library, the clones were grouped into 13 T-RFLP operational taxonomic units (OTUs). Reverse fragments generally gave less heterogeneous fragments in size. The accuracy of T-RFLP screening was evaluated by sequencing representative clones. Closely related clones ( approximately 97% similarity) could only be resolved with multiple restriction digests where forward and reverse fragments were included in the analysis. All fragments from the clone library were detected in the T-RFLP fingerprint from the complex archaeal community. We found representatives of marine group I, II and III Archaea. Thus, the recently discovered low abundant marine group III Archaea could be clearly differentiated from the other clones in our library and comprised a considerable fraction of the clone library ( approximately 12%). Therefore, our T-RFLP screening approach proved successful in characterizing novel archaeal sequences from the marine environment.

Impact of UV Radiation on Bacterioplankton Community Composition

ABSTRACT The potential effect of UV radiation on the composition of coastal marine bacterioplankton communities was investigated. Dilution cultures with seawater collected from the surface mixed layer of the coastal North Sea were exposed to different ranges of natural or artificial solar radiation for up to two diurnal cycles. The composition of the bacterioplankton community prior to exposure was compared to that after exposure to the different radiation regimes using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA and 16S ribosomal DNA. Only minor changes in the composition of the bacterial community in the different radiation regimes were detectable. Sequencing of selected bands obtained by DGGE revealed that some species of theFlexibacter-Cytophaga-Bacteroides (FCB) group were sensitive to UV radiation while other species of the FCB group were resistant. Overall, only up to ≈10% of the operational taxonomic units present in the dilution cultures appeared to be affected by UV radiation. Thus, we conclude that UV radiation has little effect on the composition of coastal marine bacterioplankton communities in the North Sea.

Relationship between Bacterioplankton Richness, Respiration, and Production in the Southern North Sea

ABSTRACT We investigated the relationship between bacterioplankton production (BP), respiration (BR), and community composition measured by terminal restriction fragment length polymorphism in the southern North Sea over a seasonal cycle. Major changes in bacterioplankton richness were apparent from April to December. While cell-specific BP decreased highly significantly with increasing bacterioplankton richness, cell-specific BR was found to be variable along the richness gradient, suggesting that bacterioplankton respiration is rather independent from shifts in the bacterial community composition. As a consequence, the bacterial growth efficiency [BGE = BP/(BP + BR)] was negatively related to bacterioplankton richness, explaining ∼43% of the variation in BGE. Our results indicate that despite the observed shifts in the community composition, the main function of the bacterioplankton, the remineralization of dissolved organic carbon to CO2, is rather stable.

Effects of environmental variation and spatial distance on Bacteria, Archaea and viruses in sub-polar and arctic waters

We investigated the influence of environmental parameters and spatial distance on bacterial, archaeal and viral community composition from 13 sites along a 3200-km long voyage from Halifax to Kugluktuk (Canada) through the Labrador Sea, Baffin Bay and the Arctic Archipelago. Variation partitioning was used to disentangle the effects of environmental parameters, spatial distance and spatially correlated environmental parameters on prokaryotic and viral communities. Viral and prokaryotic community composition were related in the Labrador Sea, but were independent of each other in Baffin Bay and the Arctic Archipelago. In oceans, the dominant dispersal mechanism for prokaryotes and viruses is the movement of water masses, thus, dispersal for both groups is passive and similar. Nevertheless, spatial distance explained 7–19% of the variation in viral community composition in the Arctic Archipelago, but was not a significant predictor of bacterial or archaeal community composition in either sampling area, suggesting a decoupling of the processes regulating community composition within these taxonomic groups. According to the metacommunity theory, patterns in bacterial and archaeal community composition suggest a role for species sorting, while patterns of virus community composition are consistent with species sorting in the Labrador Sea and suggest a potential role of mass effects in the Arctic Archipelago. Given that, a specific prokaryotic taxon may be infected by multiple viruses with high reproductive potential, our results suggest that viral community composition was subject to a high turnover relative to prokaryotic community composition in the Arctic Archipelago.

Effects of patch connectivity and heterogeneity on metacommunity structure of planktonic bacteria and viruses

Dispersal limitation is generally considered to have little influence on the spatial structure of biodiversity in microbial metacommunities. This notion derives mainly from the analysis of spatial patterns in the field, but experimental tests of dispersal limitation using natural communities are rare for prokaryotes and, to our knowledge, non-existent for viruses. We studied the effects of dispersal intensity (three levels) and patch heterogeneity (two levels) on the structure of replicate experimental metacommunities of bacteria and viruses using outdoor mesocosms with plankton communities from natural ponds and lakes. Low levels of dispersal resulted in a decrease in the compositional differences (beta diversity) among the communities of both bacteria and viruses, but we found no effects of patch heterogeneity. The reductions in beta diversity are unlikely to be a result of mass effects and only partly explained by indirect dispersal-mediated interactions with phytoplankton and zooplankton. Our results suggest that even a very limited exchange among local communities can alter the trajectory of bacterial and viral communities at small temporal and spatial scales.

Relationship of Geographic Distance, Depth, Temperature, and Viruses with Prokaryotic Communities in the Eastern Tropical Atlantic Ocean

The richness and biogeographical distribution pattern of bacterial and archaeal communities was assessed by terminal restriction fragment length polymorphism analysis of polymerase chain reaction-amplified fragments of the 16S rRNA gene at the surface (15–25xa0m depth), in the deep chlorophyll maximum layer (DCM; 50xa0m depth), and deep waters (75–1000xa0m depth) of the eastern tropical Atlantic Ocean. Additionally, prokaryotic and viral abundance and the frequency of infected prokaryotic cells (FIC) were determined along with physico-chemical parameters to identify factors influencing prokaryotic richness and biogeography. Viral abundance was highest in the DCM layer averaging 45.5u2009×u2009106xa0ml−1, whereas in the mixed surface layer and in the waters below the DCM, average viral abundance was 11.3u2009×u2009106 and 4.3u2009×u2009106xa0ml−1, respectively. The average estimate of FIC was 8.3% in the mixed surface layer and the DCM and 2.4% in deeper waters. FIC was positively related to prokaryotic and viral abundance and negatively to archaeal richness. There was no detectable effect of geographic distance (maximum distance between stations ∼4600xa0km) or differences between water masses on bacterial and archaeal community composition. Bacterial communities showed a clear depth zonation, whereas changes in archaeal community composition were related to temperature and FIC. The results indicate that planktonic archaeal virus host systems are a dynamic component of marine ecosystems under natural conditions.

Randomly amplified polymorphic DNA reveals tight links between viruses and microbes in the bathypelagic zone of the Northwestern Mediterranean Sea.

ABSTRACT The study site located in the Mediterranean Sea was visited eight times in 2005 and 2006 to collect samples from the epipelagic (5 m), mesopelagic (200 m, 600 m), and bathypelagic (1,000 m, 2,000 m) zones. Randomly amplified polymorphic DNA PCR (RAPD-PCR) analysis was used to obtain fingerprints from microbial and viral size fractions using two different primers each. Depending on the primer used, the number of bands in the water column varied between 12 to 24 and 6 to 19 for the microbial size fraction and between 16 to 26 and 8 to 22 for the viral size fraction. The majority of sequences from the microbial fraction was related to Alphaproteobacteria, Cyanobacteria, Gammaproteobacteria, Firmicutes, and Eukaryota. Only 9% of sequences obtained from the viral fraction were of identifiable viral origin; however, 76% of sequences had no close relatives in the nr database of GenBank. Only 20.1% of complete phage genomes tested in silico resulted in potential RAPD-PCR products, and only 12% of these were targeted by both primers. Also, in silico analysis indicated that RAPD-PCR profiles obtained by the two different primers are largely representative of two different subsets of the viral community. Also, correlation analyses and Mantel tests indicate that the links between changes in the microbial and viral community were strongest in the bathypelagic. Thus, these results suggest a strong codevelopment of virus and host communities in deep waters. The data also indicate that virus communities in the bathypelagic zone can exhibit substantial temporal dynamics.