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Article

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

1
Laboratory of Algology and Microbial Ecology, Nature Research Centre, Akademijos Str. 2, LT-08412 Vilnius, Lithuania
2
Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
*
Author to whom correspondence should be addressed.
Academic Editors: Dariusz Dziga and Benedykt Wladyka
Genes 2021, 12(6), 886; https://doi.org/10.3390/genes12060886
Received: 4 May 2021 / Revised: 4 June 2021 / Accepted: 7 June 2021 / Published: 8 June 2021
(This article belongs to the Special Issue Genetics and Genomics of Metabolism in Microorganisms)
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. View Full-Text
Keywords: chlorobium phages; green sulfur bacteria; gypsum karst ecosystem; Kirkilai; Lithuania; Microviridae; Natura 2000; rare ecosystems; virus diversity; Single Cell Genomics chlorobium phages; green sulfur bacteria; gypsum karst ecosystem; Kirkilai; Lithuania; Microviridae; Natura 2000; rare ecosystems; virus diversity; Single Cell Genomics
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MDPI and ACS Style

Šulčius, S.; Alzbutas, G.; Juknevičiūtė, V.; Šimoliūnas, E.; Venckus, P.; Šimoliūnienė, M.; Paškauskas, R. Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics. Genes 2021, 12, 886. https://doi.org/10.3390/genes12060886

AMA Style

Šulčius S, Alzbutas G, Juknevičiūtė V, Šimoliūnas E, Venckus P, Šimoliūnienė M, Paškauskas R. Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics. Genes. 2021; 12(6):886. https://doi.org/10.3390/genes12060886

Chicago/Turabian Style

Šulčius, Sigitas, Gediminas Alzbutas, Viktorija Juknevičiūtė, Eugenijus Šimoliūnas, Petras Venckus, Monika Šimoliūnienė, and Ričardas Paškauskas. 2021. "Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics" Genes 12, no. 6: 886. https://doi.org/10.3390/genes12060886

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