Seasonal Variation in Viral Infection Rates and Cell Sizes of Infected Prokaryotes in a Large and Deep Freshwater Lake (Lake Biwa, Japan)

Abstract

As viruses regulate prokaryotic abundance and the carbon cycle by infecting and lysing their prokaryotic hosts, the volume of infected prokaryotes is an important parameter for understanding the impact of viruses on aquatic environments. However, literature regarding the seasonal and spatial variations in the cell volume of infected prokaryotes is limited, despite the volume of the prokaryotic community varying dynamically with season and water column depth. Here, we conducted a field survey for two annual cycles in a large and deep freshwater lake (Lake Biwa, Japan), where large prokaryotes inhabit the deeper layer during the stratified period. We used transmission electron microscopy to reveal the seasonal and spatial variation in the frequency of viral infection and cell volume of infected prokaryotes. We found that the viral infection rate in the surface layer increased when estimated contact rates increased during the middle of the stratified period, whereas the infection rate in the deeper layer increased despite low estimated contact rates during the end of the stratified period. In addition, in the deeper layer, the fraction of large prokaryotes in the total and infected prokaryotic communities increased progressively while the number of intracellular viral particles increased. We suggest different ways in which the viral abundance is maintained in the two water layers. In the surface layer, it is speculated that viral abundance is supported by the high viral infection rate because of the high activity of prokaryotes, whereas in the deeper layer, it might be supported by the larger number of intracellular viral particles released from large prokaryotes. Moreover, large prokaryotes could contribute as important sources of organic substrates via viral lysis in the deeper layer, where labile dissolved organic matter is depleted.

Top-Down Controls of Bacterial Metabolism: A Case Study from a Temperate Freshwater Lake Ecosystem

“…We principally focused on lytic viruses, which through the rapid production of viral particles directly contribute to viral shunt rather than dormant temperate viruses. Viral lytic infection determined by the FVIC approach through direct observation using TEM in Lake Goule (1.2 to 3.7%) was comparable and within the typical range of those (i.e., <5%) reported for freshwater environments [7,41,46]. In contrast to reports from other freshwater systems, the absence of a relationship between the percentage of viral-infected cells and both viral and bacterial abundances indicates that the viral attack was dependent on the density of the susceptible community, rather than the density of the total host population.…”

“…Flow cytometry signatures of viral and bacterial abundances revealed that their counts were within the reported range of values for mesotrophic freshwater systems [39][40][41], with no marked fluctuation in their ratio with time and space. Irrespective of the sampled depths, viral abundance was better described by a power law function of bacterial abundance with a scaling exponent less than 1, unlike reports from other freshwater systems [7,42] indicating that viral abundance increases less than proportionately given increases in bacterial abundances as previously reported for nutrient limited systems [43].…”

Long-read-resolved, ecosystem-wide exploration of nucleotide and structural microdiversity of lake bacterioplankton genomes

“…The first was comprehensive metagenomic sampling in an ecosystem. We targeted freshwater bacterioplankton assemblages sampled spatiotemporally (2 depths × 12 months) at a pelagic station on Lake Biwa, a monomictic lake with an oxygenated hypolimnion that harbors one of the best-studied freshwater microbial ecosystems (12)(13)(14)(15)(16). The second step was long-read metagenomic assembly, which can overcome the problem of fragmented assembly using reads longer than a repeat or hypervariable region (17)(18)(19)(20).…”

Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes

“…The first was comprehensive metagenomic sampling in an ecosystem. We targeted freshwater bacterioplankton assemblages sampled spatiotemporally (2 depths  12 months) at a pelagic station on Lake Biwa, a monomictic lake with an oxygenated hypolimnion that harbors one of the best-studied freshwater microbial ecosystems (12)(13)(14)(15)(16). The second step was long-read metagenomic assembly, which can overcome the problem of fragmented assembly by using reads longer than a repeat or hypervariable region (17)(18)(19)(20).…”