Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics

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.

Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms

“…the HQ and MQ phages, 64 were from Chromatiales genomes (33 Chromatidales phages, and 31 Ectothiorhodospiraceae) (Supplementary Data 2). The majority (63) of HQ and MQ phages were classified as lysogenic, and of the eight phages classified as lytic, three were complete/circular. No Chlorobi phages were identified as lysogenic, indicating the absence of known integration enzymes in these prophages identified within their hosts' genomes.…”

“…However, the presence of phages encoding the AMGs of interest in publicly available genomes of PSB and GSB isolated from other lakes, sediments, freshwater creeks, and coastal seawater around the world (Fig. 2 and Supplementary Data 1 63 ) suggests a broad distribution and significance of these viral genes. Future work is needed to demonstrate active viral infections in the lakes studied and whether viral gene expression during infection alters host metabolic pathways as predicted here.…”

“…Publicly available bacterial genomes deposited as 'complete genome', 'scaffold', or 'contig' belonging to the two PSB families Chromatiaceae (98 genomes) and Ectothiorhodospiraceae (115 genomes), and the GSB phyla Chlorobiota (33 genomes) were retrieved from NCBI in 2022 (accession numbers available in Supplementary Data 1 63 ). Putative prophages were identified in these genomes using VIBRANT v1.2.1.…”

Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing

“…AMGs featuring functional relevance in carbon metabolism, assembly of iron-sulfur clusters, nitrification, methane oxidation, and other metabolic processes are believed to give an advantage by improving utilization of nutrients within their host [8,9]. PAPS reductase has been described to be involved in assimilatory pathways of sulfate reduction, suggesting that phages can influence the metabolism and cycling of this essential element [70,71] and thus have an impact on the biogas microbial community (Supplementary Material Table S3). Furthermore, it was hypothesized that PAPS reductase is an accessory protein belonging to the clade of CysH family enzymes associated with type-IV CRISPR-Cas systems [69], representing the bacterial and archaeal adaptive immunity systems against virus particles [72].…”

Phytoplankton Community Structure in Highly-Mineralized Small Gypsum Karst Lake (Russia)

“…On the global scale, surface outcrops of gypsiferous strata appear quite limited [7]. In this regard, such lakes are often considered as endemic [8] or unique [4][5][6]9].…”