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Viral lysis of phytoplankton is one of the most common forms of death on Earth. Building on an assay used extensively to assess rates of phytoplankton loss to predation by grazers, lysis rates are increasingly quantified through dilution-based techniques. In this approach, dilution of viruses and hosts are expected to reduce infection rates and thus increase host net growth rates (i.e., accumulation rates). The difference between diluted and undiluted host growth rates is interpreted as a measurable proxy for the rate of viral lytic death. These assays are usually conducted in volumes ≥ 1 L. To increase throughput, we implemented a miniaturized, high-throughput, high-replication, flow cytometric microplate dilution assay to measure viral lysis in environmental samples sourced from a suburban pond and the North Atlantic Ocean. The most notable outcome we observed was a decline in phytoplankton densities that was exacerbated by dilution, instead of the increased growth rates expected from lowered virus-phytoplankton encounters. We sought to explain this counterintuitive outcome using theoretical, environmental, and experimental analyses. Our study shows that, while die-offs could be partly explained by a 'plate effect' due to small incubation volumes and cells adhering to walls, the declines in phytoplankton densities are not volume-dependent. Rather, they are driven by many density- and physiology-dependent effects of dilution on predation pressure, nutrient limitation, and growth, all of which violate the original assumptions of dilution assays. As these effects are volume-independent, these processes likely occur in all dilution assays that our analyses show to be remarkably sensitive to dilution-altered phytoplankton growth and insensitive to actual predation pressure. Incorporating altered growth as well as predation, we present a logical framework that categorizes locations by the relative dominance of these mechanisms, with general applicability to dilution-based assays. [ABSTRACT FROM AUTHOR]

Summary: Plants and phytoplankton are natural sources of the volatile organic compounds (VOCs) acetone and isoprene, which are reactive and can alter atmospheric chemistry. In earlier research we reported that, when co‐cultured with a diatom, the marine bacterium Pelagibacter (strain HTCC1062; 'SAR11 clade') reduced the concentration of compounds tentatively identified as acetone and isoprene. In this study, experiments with Pelagibacter monocultures confirmed that these cells are capable of metabolizing acetone and isoprene at rates similar to bacterial communities in seawater and high enough to consume substantial fractions of the total marine acetone and isoprene budgets if extrapolated to global SAR11 populations. Homologues of an acetone/cyclohexanone monooxygenase were identified in the HTCC1062 genome and in the genomes of a wide variety of other abundant marine taxa, and were expressed at substantial levels (c. 10−4 of transcripts) across TARA oceans metatranscriptomes from ocean surface samples. The HTCC1062 genome lacks the canonical isoprene degradation pathway, suggesting an unknown alternative biochemical pathway is used by these cells for isoprene uptake. Fosmidomycin, an inhibitor of bacterial isoprenoid biosynthesis, blocked HTCC1062 growth, but the cells were rescued when isoprene was added to the culture, indicating SAR11 cells may be capable of synthesizing isoprenoid compounds from exogenous isoprene. [ABSTRACT FROM AUTHOR]