Abstract
The present study illustrates the genetic diversity of four uncultured viral communities from the surface waters of Cochin Estuary (CE), India. Viral diversity inferred using Illumina HiSeq paired-end sequencing using a linker-amplified shotgun library (LASL) revealed different double-stranded DNA (dsDNA) viral communities. The water samples were collected from four stations PR1, PR2, PR3, and PR4, during the pre-monsoon (PRM) season. Analysis of virus families indicated that the Myoviridae was the most common viral community in the CE followed by Siphoviridae and Podoviridae. There were significant (p < 0.05) spatial variations in the relative abundance of dominant families in response to the salinity regimes. The relative abundance of Myoviridae and Podoviridae were high in the euryhaline region and Siphoviridae in the mesohaline region of the estuary. The predominant phage type in CE was phages that infected Synechococcus. The viral proteins were found to be involved in major functional activities such as ATP binding, DNA binding, and DNA replication. The study highlights the genetic diversity of dsDNA viral communities and their functional protein predictions from a highly productive estuarine system. Further, the metavirome data generated in this study will enhance the repertoire of publicly available dataset and advance our understanding of estuarine viral ecology.
Highlights
Viruses are integral components of the marine microbial loop and are numerically most abundant biological entities in aquatic ecosystems[1,2,3]
The four sampling locations lie in a longitudinal transect between 76°15′ to 76°25′E and in a latitudinal transect between 9°30′ to 10°10′N, along the Cochin estuary in India (Supplementary Fig. 1)
The dissolved oxygen concentration was high during the study period throughout the estuary with higher values at PR4 (5.51 μM)
Summary
Viruses are integral components of the marine microbial loop and are numerically most abundant biological entities in aquatic ecosystems[1,2,3]. Viruses exhibit high levels of host specificity in aquatic environments and are highly diverse in terms of their morphotypes and genotypes[6] Despite their numerical abundance and ecological significance, very little is known about estuarine phage biodiversity and biogeography. Generation DNA sequencing has been widely employed in the study of viral metagenomes (viromes) in different aquatic environments including fresh water[14,15], oceans[10,16,17,18,19] and reused wastewater[20] It provides an in-depth and thorough analysis of genomics and proteomics of aquatic viruses from diverse habitats and decipher the role of viruses in aquatic ecology and biogeochemistry. This study presents a detailed report on the metaviriome analysis from a highly productive estuarine system
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