The viral component in aquatic systems clearly needs to be incorporated into future ocean and inland water climate models. Viruses have the potential to influence carbon and nutrient cycling in aquatic ecosystems significantly. Changing climate likely has both direct and indirect influence on virus-mediated processes, among them an impact on food webs, biogeochemical cycles and on the overall metabolic performance of whole ecosystems. Here we synthesise current knowledge on potential climate-related consequences for viral assemblages, virus-host interactions and virus functions, and in turn, viral processes contributing to climate change. There is a need to increase the accuracy of predictions of climate change impacts on virusdriven processes, particularly of those linked to biological production and biogeochemical cycles. Comprehension of the relationships between microbial/viral processes and global phenomena is essential to predict the influence on as well as the response of the biosphere to global change.

Flood events are now recognized as potentially important occasions for the transfer of soil microbes to stream ecosystems. Yet, little is known about these "dynamic pulses of microbial life" for stream bacterial community composition (BCC) and diversity. In this study, we explored the potential alteration of stream BCC by soil inoculation during high flow events in six pre-alpine first order streams and the larger Oberer Seebach. During 1 year, we compared variations of BCC in soil water, stream water and in benthic biofilms at different flow conditions (low to intermediate flows versus high flow). Bacterial diversity was lowest in biofilms, followed by soils and highest in headwater streams and the Oberer Seebach. In headwater streams, bacterial diversity was significantly higher during high flow, as compared to low flow (Shannon diversity: 7.6 versus 7.9 at low versus high flow, respectively, p < 0.001). Approximately 70% of the bacterial operational taxonomic units (OTUs) from streams and stream biofilms were the same as in soil water, while in the latter one third of the OTUs were specific to high flow conditions. These soil high-flow OTUs were also found in streams and biofilms at other times of the year. These results demonstrate the relevance of floods in generating short and reoccurring inoculation events for flowing waters. Moreover, they show that soil microbial inoculation during high flow enhances microbial diversity and shapes fluvial BCC even during low flow. Hence, soil microbial inoculation during floods could act as a previously overlooked driver of microbial diversity in headwater streams.

Hydrological events mobilize chemically diverse dissolved organic matter (DOM) from soils to streams. Further, such events can also cause an influx of soil microbial life into fluvial systems. Here we present results from the HYDRO-DIVERSITY project, which aims to investigate the dynamic transfer of DOM and microbial life from catchment soils to streams, as well as their downstream fate. We studied the microbial community composition and DOM quality using 16S Illumina sequencing and fluorescence and absorbance spectroscopy. Data from small streams showed strong changes in DOM composition and in the microbial community delivered from soils during hydrological events. Moreover, we performed a flume experiment, in which soil microbial inoculation and the processing of DOM across different biofilm ages were evaluated. As such, biofilm age did not directly affect the establishment of soil microbes in the stream ecosystem. However, in-stream processing of soil DOM appeared to be affected by the inoculation event. This poses the fundamental question, if the processing of DOM in streams and rivers depends on the transient presence of specific soil microbes in stream ecosystems. Overall our results show that soils provide a dynamic and relevant influx of microbes and DOM to first order streams and that this dynamic influx likely affects microbial community dynamics of downstream fluvial networks as well as in-stream DOM processing.

It is well recognized that river-floodplain systems contribute significantly to riverine ecosystem metabolism, and that bacteria are key players in the aquatic organic carbon cycle, but surprisingly few studies have linked bacterial community composition (BCC), function and carbon quality in these hydrologically highly dynamic habitats. We investigated aquatic BCC and extracellular enzymatic activity (EEA) related to dissolved organic carbon quality and algae composition, including the impact of a major flood event in one of the last remaining European semi-natural floodplain-systems. We found that surface connectivity of floodplain pools homogenizes BCC and EEA, whereas low connectivity led to increased BCC and EEA heterogeneity, supported by their relationship to electrical conductivity, an excellent indicator for surface connection strength. Hydrogeochemical parameters best explained variation of both BCC and EEA, while the algal community and chromophoric DOM properties explained only minor fractions of BCC variation. We conclude that intermittent surface connectivity and especially permanent isolation of floodplain pools from the main river channel may severely alter BCC and EEA, with potential consequences for nutrient cycling, ecological services and greenhouse gas emissions. Disentangling microbial structure–function coupling is therefore crucial, if we are to understand and predict the consequences of human alterations on these dynamic systems.

In this chapter, we summarize and discuss methods used to study viral interactions in aquatic environments. These methods to assess interactions between viruses, hosts and the environment (including other viruses) are operationally separated into interactions at the molecular, single-cell, and community levels. Many of these methods benefit from the methodological advancements in the field of molecular biology including the 'Omics area'. There are, however, numerous methods from other fields. We also present examples of unanswered questions along with problems solved by these questions. Finally, we conclude that viral interactions with the abiotic environment have received surprisingly little attention, so far, from a methodological perspective.

During the past 30 years, a vast number of articles have been published on the importance -in terms of abundance, diversity and functional roles -of viruses inhabiting the aquatic world (either marine or freshwater), which include several excellent reviews.Our knowledge, e.g. of the interactions of viruses with the living (organisms) and nonliving compartments (i.e.dissolved organic matter/ particles/nutrients/physical factors) in aquatic environments, has considerably increased.Furthermore, recent new ideas, concepts and technologies have shed light on host-virus interactions and the diversity of viral species and functions as discussed in this book.This chapter highlights some of these current advances in the field of aquatic viral ecology.Recently developed models and concepts will also be discussed, further emphasizing the role of defence mechanisms against viruses which appear to be important drivers in strain diversification of host species.Additionally, new environments such as anoxic and benthic sediments have received more attention and novel information has been gathered, e.g. on archaeal and RNA viruses.Interactions within entire food webs, such as with heterotrophic dinoflagellates, oysters and even cascading effects up to cyanobacteria-consuming flamingo populations represent another aspect of looking at viruses and their role in the global biosphere.The chapter also discusses knowledge gaps and proposes future research avenues.

River-floodplain systems are characterized by changing hydrological connectivity and variability of resources delivered to floodplain water bodies. Although the importance of hydrological events has been recognized, the effect of flooding on CH4 concentrations and emissions from European, human-impacted river-floodplains is largely unknown. This study evaluates aquatic concentrations and emissions of CH4 from a highly modified, yet partly restored river-floodplain system of the Danube near Vienna (Austria). We covered a broad range of hydrological conditions, including a 1-yr flood event in 2012 and a 100-yr flood in 2013. Our findings demonstrate that river-floodplain waters were supersaturated with CH4, hence always serving as a source of CH4 to the atmosphere. Hydrologically isolated habitats in general have higher concentrations and produce higher fluxes despite lower physically defined velocities. During surface connection, however, CH4 is exported from the floodplain to the river, suggesting that the main channel serves as an "exhaust pipe" for the floodplain. This mechanism was especially important during the 100-yr flood, when a clear pulse of CH4 was flushed from the floodplain with surface floodwaters. Our results emphasize the importance of floods differing in magnitude for methane evasion from river-floodplains; 34% more CH4 was emitted from the entire system during the year with the 100-yr flood compared to a hydrologically "normal" year. Compared to the main river channel, semi-isolated floodplain waters were particularly strong sources of CH4. Our findings also imply that the predicted increased frequency of extreme flooding events will have significant consequences for methane emission from river-floodplain systems.

The viral component in aquatic systems clearly needs to be incorporated into future ocean and inland water climate models. Viruses have the potential to influence carbon and nutrient cycling in aquatic ecosystems significantly. Changing climate likely has both direct and indirect influence on virus-mediated processes, among them an impact on food webs, biogeochemical cycles and on the overall metabolic performance of whole ecosystems. Here I synthesize current knowledge on potential climate-related consequences for viral assemblages, virus host interactions and virus function, and, in turn, viral processes contributing to climate change. There is a need to increase the accuracy of predictions of climate change impacts on virus-driven processes, particularly of those linked to biological production and biogeochemical cycles. Comprehension of the relationships between microbial/viral processes and global phenomena is essential to predict the influence on as well as the response of the biosphere to global change.

River-floodplain systems are susceptible to rapid hydrological events. Changing hydrological connectivity of the floodplain generates a broad range of conditions, from lentic to lotic. This creates a mixture of allochthonously and autochthonously derived dissolved organic matter (DOM). Autochthonous DOM, including photosynthetic extracellular release (PER), is an important source supporting bacterial secondary production (BSP). Nonetheless, no details are available regarding microbial extracellular enzymatic activity (EEA) as a response to PER under variable hydrological settings in river-floodplain systems. To investigate the relationship between bacterial and phytoplankton components, we therefore used EEA as a tool to track the microbial response to non-chromophoric, but reactive and ecologically important DOM. The study was conducted in three floodplain subsystems with distinct hydrological regimes (Danube Floodplain National Park, Austria). The focus was on the post-flood period. Enhanced %PER (up to 48% of primary production) in a hydrologically isolated subsystem was strongly correlated with β-glucosidase, which was related to BSP. This shows that-in disconnected floodplain backwaters with high terrestrial input-BSP can also be driven by autochthonous carbon sources (PER). In a semi-isolated section, in the presence of fresh labile material from primary producers, enhanced activity of phenol oxidase was observed. In frequently flooded river-floodplain systems, BSP was mainly driven by enzymatic degradation of particulate primary production. Our research demonstrates that EEA measurements are an excellent tool to describe the coupling between bacteria and phytoplankton, which cannot be deciphered when focusing solely on chromophoric DOM.

The ecology of viruses has been studied only in a limited number of rivers and streams. In light of a recent re-appraisal of the global fluvial surface area, issues such as abundance and production, host mortality and the influence of suspended particles and biofilms are addressed. Viral life cycles, potential impacts of viruses on water biochemistry and carbon flow, and viral diversity are considered. Variability in trophic levels along with the heterogeneous nature and hydrological dynamics of fluvial environments suggest a prevailingly physical control of virus-related processes under lotic conditions and more biological control under lentic conditions. Viral lysis likely contributes to a pool of rapidly cycling carbon in environments typically characterized by high proportions of recalcitrant terrestrial carbon. On average, 33.6% (equalling 0.605 Pg C year-1 ) of the globally respired carbon from fluvial systems may pass through a viral loop. Virus distribution and the proportion of organic material in horizontal transport versus processes in retention zones remain to be determined in detail. The need for up-scaling the contribution of virus-related processes in fluvial systems is of global relevance. Further, the role of climate change and the effect of anthropogenic alterations of fluvial systems on viruses require attention. The identification of these considerable knowledge gaps should foster future research efforts.

Trophic cascade effects occur when a food web is disrupted by loss or significant reduction of one or more of its members. In East African Rift Valley lakes, the Lesser Flamingo is on top of a short food chain. At irregular intervals, the dominance of their most important food source, the cyanobacterium Arthrospira fusiformis, is interrupted. Bacteriophages are known as potentially controlling photoautotrophic bacterioplankton. In Lake Nakuru (Kenya), we found the highest abundance of suspended viruses ever recorded in a natural aquatic system. We document that cyanophage infection and the related breakdown of A. fusiformis biomass led to a dramatic reduction in flamingo abundance. This documents that virus infection at the very base of a food chain can affect, in a bottom-up cascade, the distribution of end consumers. We anticipate this as an important example for virus-mediated cascading effects, potentially occurring also in various other aquatic food webs.

Spectroscopic techniques and extracellular enzyme activity measurements were combined with assessments of bacterial secondary production (BSP) to elucidate flood-pulse-linked differences in carbon (C) sources and related microbial processes in a river-floodplain system near Vienna (Austria). Surface connection with the main channel significantly influenced the quantity and quality of dissolved organic matter (DOM) in floodplain backwaters. The highest values of dissolved organic carbon (DOC) and chromophoric DOM (CDOM) were observed during the peak of the flood, when DOC increased from 1.36 to 4.37 mg l-1 and CDOM from 2.94 to 14.32 m-1. The flood introduced DOC which consisted of more allochthonously-derived, aromatic compounds. Bacterial enzymatic activity, as a proxy to track the response to changes in DOM, indicated elevated utilization of imported allochthonous material. Based on the enzyme measurements, new parameters were calculated: metabolic effort and enzymatic indices (EEA 1 and EEA 2). During connection, bacterial glucosidase and protease activity were dominant, whereas during disconnected phases a switch to lignin degradation (phenol oxidase) occurred. The enzymatic activity analysis revealed that flooding mobilized reactive DOM, which then supported bacterial metabolism. No significant differences in overall BSP between the two phases were detected, indicating that heterogeneous sources of C sufficiently support BSP. The study demonstrates that floods are important for delivering DOM, which, despite its allochthonous origin, is reactive and can be effectively utilized by aquatic bacteria in this river-floodplain systems. The presence of active floodplains, characterized by hydrological connectivity with the main channel, creates the opportunity to process allochthonous DOC. This has potential consequences for carbon flux, enhancing C sequestration and mineralization processes in this river-floodplain system.

Abundances of virus-like particles (VLPs, mostly bacteriophages) are high in aquatic environments; therefore, techniques for precise enumeration are essential in ecological monitoring. VLPs were determined after staining with SYBR Gold by conventional epifluorescence microscopy and compared to enumerations performed by confocal laser scanning microscopy (CLSM). In order to assess the potential of CLSM for viral direct counts (VDCs), we processed samples from different freshwater and marine systems. Optical sectioning by CLSM and production of an overlay picture of multiple scans enables the often uneven whole investigated filter area to be brought to the plane of focus. This allows for subsequent image analysis of digitally created high-quality images. Another advantage using the CLSM was that the short spot excitation of the stain via laser beam minimized fading of the stain. The VDC results show that there is no significant difference between the two methods. Regarding the known difficulties of viral abundance estimates on particulate material, CLSM was further applied to enumerate VLPs on a small set of marine transparent exopolymeric particles sampled from the Atlantic Ocean. Our data suggest that CLSM is a useful tool to count viruses in water samples as well as attached to certain types of aquatic aggregates.