The impact of viral lysis and grazing by flagellates on bacterioplankton production was assessed during a mesocosm experiment in the Eastern Mediterranean Sea, in response to Saharan dust (SD) vs. mixed aerosols (A) addition. The results highlight a positive effect on bacterial abundance, production and growth rate (~1.2, ~2.4 and ~1.9 –fold higher than the controls) in both SD and A, which was also confirmed by the increased portion of high DNA content bacteria (up to 48% of the bacterial community). Lytic viral production and the portion of bacterial production lost due to viral lysis were lower in SD and A after dust addition than in the controls (0.33 ± 0.17 x106 virus-like particles mL-1 h-1 and 6 ± 4%, respectively). Potential ingestion rate of bacteria by flagellates increased upon dust enrichment, but did not differ between mesocosms. Larger predators possibly down regulated flagellate abundance, and the calculated portion of bacterial production lost due to flagellate grazing was probably an artifact. Higher frequency of lysogenic cells in A compared to SD and the controls four days after dust addition may reflect faster phosphorus limitation in A, due to receiving less dissolved inorganic phosphorus and more dissolved inorganic nitrogen than SD.

The release of silver nanoparticles (AgNPs) is expected to rise in the near future, with possible negative effects on aquatic life and enhancement of microbial resistance against AgNPs. However, a realistic evaluation of the toxicity of AgNPs to the marine ecosystem is currently missing. Therefore, we designed a mesocosm experiment to assess the impact of AgNP exposure on natural microbial plankton community dynamics in a coastal marine site at environmentally relevant concentrations. We monitored changes in the composition of the planktonic community, from viruses to protists. Further, we analyzed the concentration and properties of AgNPs for the total time of exposure. We found that the addition of AgNPs even at a low dose affected the plankton communities. Specifically, the growth of Synechococcus was inhibited and bacterial community composition significantly changed. Additionally, the amount of a lysogeny-related gene increased and viral auxiliary metabolic genes that are involved in cyanobacterial photosynthesis decreased, revealing a damaged photosynthetic potential after AgNP exposure. Microbial plankton was significantly affected due to both increased dissolved silver ions and decreased AgNP size. Our results highlight that the release of AgNPs alters the functioning of the marine food web by hampering important viral and bacterial processes.

Viruses interfere with their host’s metabolism through the expression of auxiliary metabolic genes (AMGs) that, until now, are mostly studied under large physicochemical gradients. Here, we focus on coastal marine ecosystems and we sequence the viral metagenome (virome) of samples with discrete levels of human-driven disturbances. We aim to describe the relevance of viromics with respect to ecological quality status, defined by the classic seawater trophic index (TRIX). Neither viral (family level) nor bacterial (family level, based on 16S rRNA sequencing) community structure correlated with TRIX. AMGs involved in the Calvin and tricarboxylic acid cycles were found at stations with poor ecological quality, supporting viral lysis by modifying the host’s energy supply. AMGs involved in “non-traditional” energy-production pathways (3HP, sulfur oxidation) were found irrespective of ecological quality, highlighting the importance of recognizing the prevalent metabolic paths and their intermediate byproducts. Various AMGs explained the variability between stations with poor vs. good ecological quality. Our study confirms the pivotal role of the virome content in ecosystem functioning, acting as a “pool” of available functions that may be transferred to the hosts. Further, it suggests that AMGs could be used as an ultra-sensitive metric of energy-production pathways with relevance in the vulnerable coastal zone and its ecological quality.

Introduction: Marine viruses regulate microbial population dynamics and biogeochemical cycling in the oceans. The ability of viruses to manipulate hosts’ metabolism through the expression of viral auxiliary metabolic genes (AMGs) was recently highlighted, having important implications in energy production and flow in various aquatic environments. Up to now, the presence and diversity of viral AMGs is studied using -omics data, and rarely using quantitative measures of viral activity alongside.Methods: In the present study, four depth layers (5, 50, 75, and 1,000 m) with discrete hydrographic features were sampled in the Eastern Mediterranean Sea; we studied lytic viral community composition and AMG content through metagenomics, and lytic production rates through the viral reduction approach in the ultra-oligotrophic Levantine basin where knowledge regarding viral actions is rather limited.Results and Discussion: Our results demonstrate depth-dependent patterns in viral diversity and AMG content, related to differences in temperature, nutrients availability, and host bacterial productivity and abundance. Although lytic viral production rates were similar along the water column, the virus-to-bacteria ratio was higher and the particular set of AMGs was more diverse in the bathypelagic (1,000 m) than the shallow epipelagic (5, 50, and 75 m) layers, revealing that the quantitative effect of viruses on their hosts may be the same along the water column through the intervention of different AMGs. In the resource- and energy-limited bathypelagic waters of the Eastern Mediterranean, the detected AMGs could divert hosts’ metabolism toward energy production, through a boost in gluconeogenesis, fatty-acid and glycan biosynthesis and metabolism, and sulfur relay. Near the deep-chlorophyll maximum depth, an exceptionally high percentage of AMGs related to photosynthesis was noticed. Taken together our findings suggest that the roles of viruses in the deep sea might be even more important than previously thought as they seem to orchestrate energy acquisition and microbial community dynamics, and thus, biogeochemical turnover in the oceans.