Viral Metagenomics Reveals Widely Diverse Viral Community of Freshwater Amazonian Lake

Abstract

Despite the importance of understanding the ecology of freshwater viruses, there are not many studies on the subject compared to marine viruses. The microbiological interactions in these environments are still poorly known, especially between bacteriophages and their host bacteria and between cyanophages and cyanobacteria. Lake Bologna, Belém, capital of the Brazilian State of Pará, is a water source that supplies the city and its metropolitan region. However, it remains unexplored regarding the contents of its virome and viral diversity composition. Therefore, this work aims to explore the taxonomic diversity of DNA viruses in this lake, especially bacteriophages and cyanophages, since they can act as transducers of resistance genes and reporters of water quality for human consumption. We used metagenomic sequencing data generated by previous studies. We analyzed it at the taxonomic level using the tools Kraken2, Bracken, and Pavian; later, the data was assembled using Genome Detective, which performs the assembly of viruses. The results observed here suggest the existence of a widely diverse viral community and established microbial phage-regulated dynamics in Lake Bolonha. This work is the first ever to describe the virome of Lake Bolonha using a metagenomic approach based on high-throughput sequencing, as it contributes to the understanding of water-related public health concerns regarding the spreading of antibiotic resistance genes and population control of native bacteria and cyanobacteria.

Keywords: Amazon; Lake Bolonha; bacteriophages; cyanophages; freshwater; metagenomics; virome; viruses.

Figure 1

Map of the lake area and identification of sampling points (P1, P2, and P3). Alves et al. (33).

Figure 2

Sankey diagram display of the taxonomic diversity found at samples P1 (red “viruses” tag), P2 (coral “viruses” tag), and P3 (green “viruses” tag), respectively.

Figure 3

Bar graph showing the distribution of reads for each top 20 virophages found in sample P1, plotted against their respective representations on samples P2 and P3.

Figure 4

Bar graph showing the distribution of reads for each top 20 virophages found in sample P2, plotted against their respective representations on samples P1 and P3.

Figure 5

Bar graph showing the distribution of reads for each top 20 virophages found in sample P3, plotted against their respective representations on samples P1 and P2.

Figure 6

Venn diagram showing the overlap between the top 20 viruses for samples P1 (in red), P2 (in green), and P3 (in blue).