Deep sea viruses: the dark matter in the dark ocean

Written by Markus G. Weinbauer, Lanlan Cai and Rui Zhang

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    Viruses (and microorganisms in general) are typically still regarded by the public as pathogens, as danger that has to be fought against, eradicated whenever possible. That’s especially in Covid-19 times. However, people start to realize that we need these microbes. They help for our health and provide a lot of ecosystems functions. Without their activity in processing organic matter, the ocean would not be liquid but a thick gel. The current understanding of viruses in the ocean is that they are catalysts of nutrient cycling and lubricate the food web. Ain’t that a good thing?

     It is said that people know more about the surface of the moon than about the deep sea plains. And certainly we know more about the deep sea sediments than about the dark ocean, i.e. the water column below ca. 200m where there is no photosynthesis anymore, although this oceanic realm contains ca. 75% of the prokaryotic biomass. Metagenomic studies have shown that the dark ocean is one of the 4-5 viral biomes in the ocean {Gregory et al., 2019, Cell}. Howevere, > 90% of the sequences in viral metagenomes do not have a match in data bases from isolated and described viruses. To get a handle on this big unknown is a big challenge for the years to come.

     Getting samples from the deep sea is time and money consuming. Experiments or sample analysis in the lab are typically done within a day or week. To get just to sampling points for the dark ocean typically takes a day or a week (or more). Then you have to lower down sampling devices such as Niskin bottles mounted in a CTD-carousel (CTD stands for sensors measuring conductivity, temperature, density) which can be closed at desired depths. That takes again hours. And the water sample is usually limited to 100-200 liters. Usually the water samples are processed right away for analyses that are not made onboard but have to wait until the ship is back in a harbour. Ship-time is too expensive and ship-space is too limited to do large-scale analysis onboard (at least for biological parameters).

     However, we can do experiments. That’s what we did with a water sample collected from 2,000m in the western Pacific Ocean. Using tangential flow filtration, a water sample was diluted with a fraction containing viruses (<0.22 µm pore-size filtrate) or a fraction of seawater where viruses had been removed (<30 kDa filtrate). The presence of viruses controlled biomass and sustained the diversity of bacterioplankton in similar ways as has been shown previously for surface marine waters.

    Surpisingly, the presence of viruses reduced the positive correlations for potentially active bacteria (RNA based analysis) but increased the complexity and clustering (DNA based analysis). This could mean that viruses increase system diversity (hence stability) by preventing that a few bacterial species take over. Anyways, the data clearly indicate that viruses have strong impact on the interactions of bacterioplankton in the deep ocean.     Viruses in the deep ocean will likely continue to reveal surprises ; hopefully more pleasant ones than we experience right now during the pandemic.



Rui Zhang

Professor, Xiamen University

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