Abstract
Little is known about the diversity and distribution of viruses infecting green sulfur bacteria (GSB) thriving in euxinic (sulfuric and anoxic) habitats, including gypsum karst lake ecosystems. In this study, we used targeted cell sorting combined with single-cell sequencing to gain insights into the gene content and genomic potential of viruses infecting sulfur-oxidizing bacteria Chlorobium clathratiforme, obtained from water samples collected during summer stratification in gypsum karst Lake Kirkilai (Lithuania). In total, 82 viral contigs were bioinformatically identified in 62 single amplified genomes (SAGs) of C. clathratiforme. The majority of viral gene and protein sequences showed little to no similarity with phage sequences in public databases, uncovering the vast diversity of previously undescribed GSB viruses. We observed a high level of lysogenization in the C. clathratiforme population, as 87% SAGs contained intact prophages. Among the thirty identified auxiliary metabolic genes (AMGs), two, thiosulfate sulfurtransferase (TST) and thioredoxin-dependent phosphoadenosine phosphosulfate (PAPS) reductase (cysH), were found to be involved in the oxidation of inorganic sulfur compounds, suggesting that viruses can influence the metabolism and cycling of this essential element. Finally, the analysis of CRISPR spacers retrieved from the consensus C. clathratiforme genome imply persistent and active virus–host interactions for several putative phages prevalent among C. clathratiforme SAGs. Overall, this study provides a glimpse into the diversity of phages associated with naturally occurring and highly abundant sulfur-oxidizing bacteria.
Highlights
Lakes of gypsum karst are small, yet very complex, aquatic ecosystems formed in sinkholes that emerge due to the erosion of gypsiferous dolomite bedrock
Bacterial community composition in Lake Kirkilai was examined by 16S rRNA gene amplicon sequencing of water samples collected at four different depths: at the surface (1 m) and in the euxinic zone at 3 m, 4 m, and 5 m depth; predefined by the in situ measurements of environmental variables (Table S1)
To further evaluate the diversity of C. clathratiforme single amplified genomes (SAGs)-associated viruses, we focused on eight medium- and high-quality viral contigs, including two complete and five draft genomes classified as members of Caudovirales (Table S4), and one complete genome of the Microviridae family phage
Summary
Lakes of gypsum karst are small, yet very complex, aquatic ecosystems formed in sinkholes that emerge due to the erosion of gypsiferous dolomite bedrock. These endemic lakes can be characterized by strong thermal and chemical stratification, leading to contrasting gradients in redox potential and microbial metabolism [1,2]. There is a strong need to explore the diversity and genomic potential of phages in the context of the prevailing microbial assemblages throughout the environmental gradients of the karst lake ecosystems, and, more importantly, to identify the existing links between different members of viral and bacterial communities
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