RNA-Seq Virus Fraction in Lake Baikal and Treated Wastewaters
Abstract
:1. Introduction
2. Results
2.1. Assessment of Microbial Quality of Effluent Wastewater and Water in Lake Baikal
2.2. General Information
2.3. DNA Viruses
2.3.1. NR Database
2.3.2. IMG/VR Database
2.4. RNA Viruses
2.4.1. NR Database
2.4.2. IMG/VR Database
2.5. RNA-Dependent RNA Polymerase Analysis
2.6. Search for the Complete Genomes of Viruses
2.7. Identification of Human and Animal Viruses
2.7.1. Human Viruses
2.7.2. Animal Viruses
2.8. Cluster Analysis of Transcriptomes
2.9. Functional Analyses of Viral and Non-Viral ORFs
2.9.1. VOG Database
- In pelagic samplesBacterial domain—63.9–100% (median—100%), with various representatives of Actinobacteria, Proteobacteria, Firmicutes, Nitrospirae, and the eukaryote (99.6–100%) Malassezia restricta.
- In treated wastewaterBacterial domain—47.7–100% (median 99.8%), with Actinobacteria; Proteobacteria; Firmicutes; Bacteroidetes; Verrucomicrobia; Nitrospirae; and eukaryotes (33.1–100%), such as Malassezia restricta, Symbiodinium microadriaticum, and Brachionus angularis.
- In pelagic samplesStaphylococcus phage PhiSepi-HH3, putative ABC transporter ATP-binding protein (QPB07827) with up to 99.4% aa identity; Klebsiella phage ST11-VIM1phi8.2, peptide transport system ATP-binding protein—up to 92.3%; Planktothrix phage PaV-LD, ABC transporter (ADZ31540)—up to 65.5% identity and others; similarity range from 24.9 to 99.4% (median 36.3%).
- In treated wastewaterStreptococcus phage MissG2, UvrABC system protein A (UJD17646) up to 71.1% aa identity; Escherichia phage vB_EcoS-640R1, lipoprotein-releasing system ATP-binding protein (URC10021) up to 70.3%; Klebsiella phage ST11-VIM1phi8.2 (QBP28525.1) up to 64.1%; and others.
2.9.2. KEGG Database
- Glutamine synthetase (an essential enzyme in cellular nitrogen metabolism);
- Acetyl-CoA C-acetyltransferase (an enzyme that catalyzes the final step of fatty acid oxidation).
- The 2-oxoglutarate dehydrogenase E1 component (involved in the tricarboxylic acid cycle);
- Acetolactate synthase I/II/III large subunit (a protein found in plants and microorganisms that catalyzes the first step in the synthesis of branched-chain amino acids).
- RVP4—chromosome partitioning protein (required for efficient plasmid and chromosome partitioning in many bacterial species);
- RVP5, SevRVP22_08—DNA gyrase subunit A (belongs to the group of topoisomerases);
- RVP6—DNA segregation ATPase FtsK/SpoIIIE (mediates proper chromosome segregation in dividing bacteria);
- SRVP22_05—elongation factor G (prokaryotic elongation factor involved in protein translation);
- SluRVP22_08—DNA gyrase subunit B.
- In the RVP4, RVP5, RVP6, SevRVP22_08, and SluRVP22_08 samples—the ABC-2 type transport system ATP-binding protein;
- In SRVP22_05—OmpA-OmpF porin, the OOP family (the most abundant in the outer membranes of many Gram-negative bacteria).
- In the RVP4 and SevRVP22_08 samples—leucyl-tRNA synthetase;
- In RVP5, RVP6—isoleucyl-tRNA synthetase;
- In SRVP22_05—large subunit ribosomal protein L2;
- In SluRVP22_08—large subunit ribosomal protein L14.
3. Discussion
4. Materials and Methods
4.1. Sample Collection
4.2. Sample Preparation
4.3. Bioinformatic Analyses
4.4. Sanitary/Microbiological Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample | TC, CFU/100 cm3 | E. coli, CFU/100 cm3 | Enterococci, CFU/100 cm3 | Coliphages, PFU/100 cm3 |
---|---|---|---|---|
Slyudyanka, May 2022 | 2000 | 0 | 24 | 0 |
Slyudyanka, August 2022 | 800,000 | 800,000 | 80,000 | 16,200 |
Severobaikalsk, August 2022 | 900 | 0 | 16 | 0 |
Sample | DNA Viruses, % | RNA Viruses, % |
---|---|---|
RVP4 | 95.4 | 4.6 |
RVP5 | 98.1 | 1.9 |
RVP6 | 99.5 | 0.5 |
SevRVP22_08 | 90.8 | 9.2 |
SluRVP22_08 | 74.2 | 25.8 |
SRVP22_05 | 39.6 | 60.4 |
Sample | Virus | Protein | Amino Acid Identity, % | Host |
---|---|---|---|---|
RVP4 | Dicistroviridae sp. | QJI52080, capsid polyprotein | 84.4 | Drosophilidae |
SRVP22_05 | Drosophila C virus | NP_044946, capsid polyprotein | 74.5–87.2 | Drosophilidae |
Otarine picobirnavirus | AMP18960, RdRp | 59.8–81.3 | Otariidae | |
Bovine picobirnavirus | ATY68940, RdRp | 78.1–87.9 | Bovidae | |
Porcine picobirnavirus | ASM93467, RdRp | 69.1–82.9 | Suidae | |
SluRVP22_08 | Drosophila C virus | QEQ50987, replicase polyprotein | 74.5–89.3 | Drosophilidae |
Bactrocera dorsalis picorna-like virus | QMU95558, putative polyprotein | 55.4–74.6 | Tephritidae | |
Big Sioux River virus | ATI98941, structural protein precursor | 83 | Aphididae | |
Apis mellifera associated microvirus 2 | AZL82703, major capsid protein | 74.9 | Apidae | |
Soybean thrips picorna-like virus 9 | QQP18733, polyprotein | 79.5 | Thripidae | |
Fox picobirnavirus | AGK45545, RdRp | 56.6–64.7 | Canidae | |
Otarine picobirnavirus | AMP18960, RdRp | 77 | Otariidae | |
Bovine picobirnavirus | AYF57589, RdRp | 70.2–76 | Bovidae | |
Picobirnavirus sp. | QQM99847, putative capsid | 29.1–66.7 | Cervidae | |
Porcine picobirnavirus | ASM93458, capsid protein | 68.4–91.9 | Suidae | |
Phylloscopus inornatus ambidensovirus | QVW56839, MAG: putative structural protein VP1 | 65.7 | Phylloscopidae |
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Potapov, S.; Gorshkova, A.; Krasnopeev, A.; Podlesnaya, G.; Tikhonova, I.; Suslova, M.; Kwon, D.; Patrushev, M.; Drucker, V.; Belykh, O. RNA-Seq Virus Fraction in Lake Baikal and Treated Wastewaters. Int. J. Mol. Sci. 2023, 24, 12049. https://doi.org/10.3390/ijms241512049
Potapov S, Gorshkova A, Krasnopeev A, Podlesnaya G, Tikhonova I, Suslova M, Kwon D, Patrushev M, Drucker V, Belykh O. RNA-Seq Virus Fraction in Lake Baikal and Treated Wastewaters. International Journal of Molecular Sciences. 2023; 24(15):12049. https://doi.org/10.3390/ijms241512049
Chicago/Turabian StylePotapov, Sergey, Anna Gorshkova, Andrey Krasnopeev, Galina Podlesnaya, Irina Tikhonova, Maria Suslova, Dmitry Kwon, Maxim Patrushev, Valentin Drucker, and Olga Belykh. 2023. "RNA-Seq Virus Fraction in Lake Baikal and Treated Wastewaters" International Journal of Molecular Sciences 24, no. 15: 12049. https://doi.org/10.3390/ijms241512049