Characteristic of Lake Baikal viromes using high-throughput sequencing
February — December 2021
The virome is a pool of DNA sequences belonging to viruses, the study of which will help to assess viral diversity and determine which viruses are present, including the identification of pathogenic and opportunistic viruses.
The main point and advantage of obtaining a virome is the answer to the question «Who is here?» the entire pool of viral DNA gives an idea of the composition of the viral community. As you know, the composition of the community determines its role in the ecosystem, so the solution of the first question sheds light on the next question: «What do they do?». The search for potentially dangerous viruses using modern methods is an integral part of ecosystem monitoring, which can help identify and identify threat viruses. The diversity of viruses and the structure of viral communities in aquatic ecosystems are still not well understood, despite the complex of applied methods and approaches. Most of the published works on aquatic viruses, including bacteriophages, refer to marine and oceanic ecosystems and, to a lesser extent, to fresh waters. Studies of viral communities using modern methods of genetic analysis are of particular relevance.
Lake Baikal Foundation’s project assesses the genetic and taxonomic diversity, and structure of the viral community in the pelagic zone of Lake Baikal using high-throughput sequencing and bioinformatics methods.
The research is carried out under the lead of Sergey Potapov, the winner of the Baikal Initiative grant competition for young scientists.
Goal:
- to investigate the genetic diversity of viruses in Lake Baikal, to determine their taxonomic composition and the ratio of taxa, to replenish the data of virome studies from freshwater lakes, to identify potentially dangerous groups of viruses in Lake Baikal.
Tasks:
- to provide grant support to the Limnological Institute Siberian Branch of the Russian Academy of Sciences for the project implementation;
- to conduct the following works in 2021 within the grant support:
1) to carry out the genetic analysis of a diversity of viruses in Lake Baikal using high-throughput sequencing and bioinformatics methods;
2) to carry out an assessment of the genetic and taxonomic composition, structure of the viral community in the pelagic zone of Lake Baikal in the autumn, to conduct a comparative study with viromes obtained earlier also from other reservoirs;
3) to carry out an assessment of the viral communities of Lake Baikal on the content of potentially dangerous viruses, to analyze the possible threat of biological pollution of the biota of the lake by the ingress of microorganisms of anthropogenic origin from wastewater.
What has been done:
- Water sampling in June and September 2021 at the central station of the section Listvyanka village — Tankhoi village. Samples were taken at 3.5 l from the surface of 5, 10, 15, 25 and 50 m, then mixed to obtain an integral sample. A total of 21 liters were taken in June and 21 liters in September.
- Filtration of the sample through special filters and concentration to obtain virus particles.
- Genetic analysis of the diversity of viruses in Lake Baikal using high-throughput sequencing and bioinformatics methods.
Results:
- During the implementation of the project, it was revealed that the dominant families of viruses in the viromes of Lake Baikal are Myoviridae, Siphoviridae, Podoviridae, Phycodnaviridae, Autographiviridae, Lavidaviridae, Mimiviridae, accounting for 95% of all identified families, with the main share belonging to bacteriophages from the order Caudovirales (up to 90%) .
- Among eukaryotic viruses, the families Phycodnaviridae (7.3-11.1%), infecting algae, and Mimiviridae (1.2-1.9%), infecting amoebas, dominated.
- Functional analysis of genes revealed the predominance of category 1 level «Phages, prophages, transposons», which indicates the intensive participation of bacteriophages in the microbial community.
- In contigs from the LTJ and LTS viromes belonging to viruses, 145 and 169 auxiliary metabolic genes (AMGs), respectively, were found.
- Shannon’s virome alpha diversity index was high and consistent with that of Lake Michigan (USA) and Han River (South Korea). The analysis of β-diversity revealed that viromes from Lake Baikal cluster together and form a common clade with viromes from other freshwater ecosystems.