Impact of Viral Lysis on the Composition of Bacterial Communities and Dissolved Organic Matter in Deep-Sea Sediments

Abstract

Viral lysis is a main mortality factor for bacteria in deep-sea sediments, leading to changing microbial community structures and the release of cellular components to the environment. Nature and fate of these compounds and the role of viruses for microbial diversity is largely unknown. We investigated the effect of viruses on the composition of bacterial communities and the pool of dissolved organic matter (DOM) by setting up virus-induction experiments using mitomycin C with sediments from the seafloor of the Bering Sea. At the sediment surface, no substantial prophage induction was detected, while incubations from 20 cm below seafloor showed a doubling of the virus-to-cell ratio. Ultra-high resolution mass spectrometry revealed an imprint of cell lysis on the molecular composition of DOM, showing an increase of molecular formulas typical for common biomolecules. More than 50% of these compounds were removed or transformed during incubation. The remaining material potentially contributed to the pool of refractory DOM. Next generation sequencing of the bacterial communities from the induction experiment showed a stable composition over time. In contrast, in the non-treated controls the abundance of dominant taxa (e.g., Gammaproteobacteria) increased at the expense of less abundant phyla. Thus, we conclude that viral lysis was an important driver in sustaining bacterial diversity, consistent with the “killing the winner” model.

Deciphering the Virus Signal Within the Marine Dissolved Organic Matter Pool

“…This so called 'viral shunt' causes the release of large amounts of cell material in form of particulate and DOM and high numbers of newly produced virus particles into the environment (Wilhelm and Suttle, 1999;Suttle, 2007). In recent years, the composition and turnover of virus-mediated lysates of different marine organisms was increasingly investigated, for example in single cyanobacterial strains (Ankrah et al, 2014;Ma et al, 2018;Zhao et al, 2019;Zheng et al, 2021), benthic bacterial communities (Heinrichs et al, 2020) and eukaryotic phytoplankton (Kuhlisch et al, 2021). This lysate was coined virus-induced DOM (vDOM) by Zhao et al (2019) and is composed of cell material in particulate and dissolved form as well as virus particles.…”

An Advanced Protocol for the Quantification of Marine Sediment Viruses via Flow Cytometry

“…The sediments were retrieved by using a multicorer (Octopus, Kiel, Germany) along a transect spanning from 40° S to 58° N close to the 180° meridian during two consecutive research cruises aboard RV Sonne (expeditions SO248 and SO254). Detailed sample retrieval and preparation are described in Heinrichs et al [ 26 ]. In brief, sediment slurries (mixed 1:1 with artificial seawater) were prepared from sediment cores sampled from the upper 20 cm of the seafloor (water depths between 3000 and >5000 m).…”

The Post-COVID-19 Era: Interdisciplinary Demands of Contagion Surveillance Mass Spectrometry for Future Pandemics

“…Van Krevelen diagrams (vKd) may offer an example of the utility of such analysis. vKd has been used to explore polymer degradation in urban waste (e.g., [49]), of dissolved organic matter (DOM) in oceanographic samples (e.g., [50]) and, more recently, to study the impact of viral activity in marine bacterial communities in DOM [51]. The latter study demonstrates the utility of vKd to measure molecular changes within DOM, as a signature of viral infection in prokaryotic cells (Figure 2).…”

“…The DOM study [51] indicates that vKd could also be employed for plotting mass patterns of unfractionated SARS-CoV-2 samples, i.e., from purified (non-degraded) viral strain to increasingly degraded strains due to environmental factors (e.g., UV exposure, heat, etc.). A vKd for a SARS-CoV-2 can have an archetypal elemental ratio pattern demonstrating typical data point pattern of lipids, proteins, genomic molecules and other biomolecules, as shown in Figure 2B.…”