[1] Shallow microtidal basins are characterized by extensive areas of tidal flats that lie within specific ranges of elevation. These landforms are inherently flat and their evolution strongly depends on the balance between sedimentary and erosive processes. Here we present a stochastic point model for tidal flat evolution to study the influence of tidal currents and wind waves on tidal flat equilibrium. The model accounts for sediment deposition and sediment resuspension by wind waves and is applied to the Venice lagoon, Italy. Model results show that the equilibrium elevation of tidal flats depends on the relationship between shear stress caused by wind waves and depth. It is found that wind wave shear stresses peak for a specific water depth which is a function of the local wave climate and fetch distance. Above this critical depth, tidal flats are unstable, since an increase in elevation reduces wave height and therefore erosion, preventing the system from recovering equilibrium conditions. The critical depth for equilibrium depends on fetch distance but not on substrate characteristics and, for the Venice lagoon, varies from À1.5 m for unlimited fetch (>3000 m) to À0.6 m for a fetch of 1000 m. The sediment characteristics determine instead the sediment input necessary to maintain the tidal flat in equilibrium at a specific elevation. Sediment inputs for tidal flats composed of fine sand need to be much higher than those required for tidal flats composed of cohesive material. Finally, we show that the spring-neap modulation of the tide is critical for tidal flat equilibrium, with erosive events occurring mostly during spring conditions that equilibrate the sediment deposition during neap tide.

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Aquatic viruses have been extensively studied over the past decade, yet fundamental aspects of freshwater virus communities remain poorly described. Our goal was to characterize virus communities captured in the >0.22 µm size-fraction seasonally and spatially in a freshwater harbour. Community DNA was extracted from water samples and sequenced on an Illumina HiSeq platform. Assembled contigs were annotated as belonging to the virus groups (i.e., order or family) Caudovirales, Mimiviridae, Phycodnaviridae, and virophages (Lavidaviridae), or to other groups of undefined viruses. Virophages were often the most abundant group, and discrete virophage taxa were remarkably stable across sites and dates despite fluctuations in Mimiviridae community composition. Diverse Mimiviridae contigs were detected in the samples and the two sites contained distinct Mimiviridae communities, suggesting that Mimiviridae are important algal viruses in this system. Caudovirales and Phycodnaviridae were present at low abundances in most samples. Of the 18 environmental parameters tested, only chlorophyll a explained the variation in the data at the order or family level of classification. Overall, our findings provide insight into freshwater virus community assemblages by expanding the documented diversity of freshwater virus communities, highlighting the potential ecological importance of virophages, and revealing distinct communities over small spatial scales.

Inspired by recent discoveries of the prevalence of large viruses in the environment, we re-assessed the longstanding approach of filtering water through small pore-size filters to separate viruses from cells before metagenomic analysis. We collected samples from three sites in Hamilton Harbour, an embayment of Lake Ontario, and studied 6 datasets derived from < 0.45 μm and > 0.45 μm size fractions to compare the diversity of viruses in these fractions. At the level of virus order/family we observed highly diverse and distinct virus communities in the > 0.45 μm size fractions, whereas the < 0.45 μm size fractions were comprised primarily of Caudovirales. The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions with higher relative abundances of cyanophages in the > 0.45 μm size fractions potentially indicating replication within cells during ongoing infections. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae and Poxviridae were detected exclusively in the often disregarded > 0.45 μm size fractions. In addition to observing unique virus communities associated with each size fraction from every site we examined, we detected viruses common to both fractions suggesting that these are candidates for further exploration because they could be the product of ongoing or recent lytic events. Most importantly, our observations indicate that analysis of either fraction alone provides only a partial perspective of dsDNA viruses in the environment, highlighting the need for more comprehensive approaches for analyzing virus communities inferred from metagenomic sequencing. IMPORTANCE Most studies of aquatic virus communities analyze DNA sequences derived from the smaller, “free virus” size fraction. Our study demonstrates that analysis of virus communities using only the smaller size fraction can lead to erroneously low diversity estimates for many of the larger viruses such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, whereas analyzing only the larger, > 0.45 μm size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data shows that examining only the smaller size fraction can lead to underestimations of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.