New Viral Biogeochemical Roles Revealed Through Metagenomic Analysis of Lake Baikal

Abstract

24Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have 25 described the microbial composition of this habitat but the viral communities from this ecosystem 26 have not been characterized in detail. Here we describe the viral diversity of this habitat across 27 depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived 28 from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, 29 2 such as Nitrospirota, Methylophilaceae and Crenarchaeota. Diversity analysis revealed significant 30 changes in viral community composition between epipelagic and bathypelagic zones. Analysis of 31 the gene content of individual viral populations allowed us to describe one of the first 32 bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes 33 that might enhance carbon fixation through the reductive TCA cycle. We also described 34 bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the 35 S-adenosyl-L-methionine cycle. These findings unraveled new ways by which viruses influence the 36 carbon cycle in freshwater ecosystems, namely by using auxiliary metabolic genes that act upon 37 metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the 38 processes through which viruses can impact biogeochemical cycles of major ecological relevance. 39 40 reductive TCA cycle; Methylotrophy; S-adenosyl-L-methionine cycle 42 43 Phycodnaviridae (1,195), and Podoviridae (809). The presence of viruses of eukaryotes in our 132 dataset derives from the fact that samples were not pre-filtered to remove eukaryotic cells. 133Computational host prediction followed by manual curation allowed putative hosts at the taxonomic 134 level of domain to be assigned to 2,870 viral sequences. These predictions suggested that the 135 majority of these sequences belonged to viruses that infect Bacteria (2,135), but viruses that infect 136 Archaea (29), Eukaryotes (621) and even virophages (85) were also identified. Among those 137 assigned as viruses of bacteria (i.e. bacteriophages) the majority of sequences were predicted to 138 infect Actinobacteria (640), followed by Proteobacteria (375), Bacteroidota (241) and 139Cyanobacteria (226). Although less frequent, some sequences were predicted to be derived from 140

Metatranscriptomics reveals declines in ice cover influence winter viral community activity

“…As top-down controls, viruses influence microbial community structure (2) and the movement of organic matter via the "viral shunt" and "viral shuttle" (3,4). Viruses also modulate the metabolism of infected cells by hijacking host cell physiology and through virusencoded metabolic genes (5), which can have far-reaching implications on biogeochemical cycles (6)(7)(8)(9). As many of Earth's aquatic ecosystems are faced with unprecedent changes in climate (10,11), there is growing interest in how viral communities are influenced by or amplify climate change and in their incorporation into predictive models (12).…”