New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal

Abstract

Background Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characterized in detail. Results Here, we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae, and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle. Conclusions These findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely, by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance.

Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake

“…Viruses were also assigned to their putative hosts by comparing the shared genetic content between viruses and hosts described in Coutinho et al (2020). Bacterial and Archaeal genomes from the NCBI RefSeq database were used as reference genomes.…”

“…GTDB was used to assign taxonomy to the reference genomes. CRISPR spacers (three points), homology matches (two points), and shared tRNAs (one point) were analyzed as virushost association signals as described in Coutinho et al (2020).…”

“…These genes, AMG, are involved in various metabolisms, including sulfur, nitrogen, and methane, in DNA replication, repair, recombination, and amino acid biosynthesis, and are also detected in extreme environments (Anantharaman et al, 2014;Anderson et al, 2014;Ahlgren et al, 2019). AMGs interfering with carbon fixation and methylotrophy metabolism have been detected in viruses from the lake Baikal (Coutinho et al, 2020). AMGs encoding photosynthetic reaction centers in cyanophages highlight their potential to boost photosynthetic metabolism (Sullivan et al, 2006;Lindell et al, 2007).…”

Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics

“…Therefore, the viral communities in shallow and deep-water regions, as well as in the southern and central basins, also significantly differ ( p -value < 0.05). A recent study [ 75 ] showed a vertical distribution and significant changes between epipelagic and bathypelagic Baikal viral community composition recovered from cellular metagenomes (fraction more than 0.22 μm). Accordingly, the difference between deep-water samples V1, V2, and V4 from other Baikal ones is partly explained by the presence of bathypelagic viral communities in them.…”

The Novel Halovirus Hardycor1, and the Presence of Active (Induced) Proviruses in Four Haloarchaea

“…Viruses of prokaryotes are extraordinarily numerous in aquatic environments [ 1 , 2 ], commonly outnumbering cells by a factor of 5 to 10 [ 3 ]. They play significant roles in a variety of important biological and biogeochemical processes, including the lysis of cells and the consequent release of organic matter, selective sweeps of prokaryotic populations that drive the evolution of both virus and host, the acceleration of genetic exchange and the redirection of host metabolism [ 4 ]. They continue to provide a source of surprising new discoveries and insights, such as the BREX (BacteRiophage EXclusion) defense system [ 5 ] of bacteria and the viral counter defense to this based on the DNA mimic protein Ocr [ 6 ].…”