Insight into bacterial diversity in gypsum karst Lake Kirkilai during summer stratification

This study reports the analysis of 16S rRNA gene amplicon sequencing data obtained from water samples collected during summer stratification in Lake Kirkilai, a unique gypsum karst lake ecosystem. In general, Actinobacteria, Chlorobi and Proteobacteria were the most abundant phyla, whereas relative distribution of different genera varied significantly across vertical gradient of the water column. No relationship between environmental variables and microbial community composition was observed. Only two taxa, Chlorobium and Rhodoluna, significantly (42-67%) contributed to the differences between samples. This suggests low (or no) structural redundancy in bacterial community, implying high vulnerability of this ecosystem to environmental perturbations. Apart from 16S sequencing, we used targeted cell sorting in combination with single-cell sequencing to gain insights into 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 existence of vast diversity of previously-undescribed GSB viruses. All C. clathratiforme SAGs clustered into a single discrete group at 99% identity threshold, suggesting rather clonal diversity of the population. We observed high level of lysogenisation of C. clathratiforme population as 54 out of 62 SAGs (87%) contained intact prophages. Among twenty-eight identified auxiliary metabolic genes (AMGs), two, thiosulfate sulfurtransferase (TST) and thioredoxin-dependent phosphoadenosine phosphosulfate (PAPS) reductase (cysH), were found to be involved in oxidation of inorganic sulfur compounds, suggesting that viruses can influence the metabolism and cycling of this important element. Finally, 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 diversity of phages associated with naturally occurring and highly abundant sulphur-oxidizing bacteria.