New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal
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RESEARCH
Open Access
New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal F. H. Coutinho1* , P. J. Cabello-Yeves1, R. Gonzalez-Serrano1, R. Rosselli2,3, M. López-Pérez1, T. I. Zemskaya4, A. S. Zakharenko4, V. G. Ivanov4 and F. Rodriguez-Valera1,5
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. Keywords: Lake Baikal, Bacteriophages, Metagenomes, Auxiliary metabolic genes, Nitrospira, Reductive TCA cycle, Methylotrophy, S-adenosyl-L-methionine cycle
Background Lake Baikal is the largest and deepest lake on Earth [1, 2]. Its uniqueness also lies in its extreme oligotrophy, icecovered periods of up to 4–4.5 months per year, and an oxic water column throughout all depths [3]. The lake is permanently mixed and only undergoes stratification for a brief period of time during summer in its first 100 m [4]. * Correspondence: [email protected] 1 Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550 Alicante, Spain Full list of author information is available at the end of the article
The surface of Lake Baikal freezes during winter, so that below the ice layer water temperatures approach 0 °C while towards deeper waters temperature raises slightly to a maximum of 4 °C. In spring, the ice layer melts, and surface water temperature raises to nearly 12 °C, only to decrease rapidly towards deeper waters (below 50 m) to the same 4 °C that are kept all year around for the deep water mass. Recent metagenomic studies have analyzed the microbiome of sub-ice epipelagic and bath
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