Metagenomic phage biodiversity: New insight into the tropical estuarine ecosystem process and microbial risk assessment

Abstract

Viruses infecting unicellular organisms were shown to have a significant influence on aquatic ecosystem processes. Their role in biogeochemical cycles, primary production and microbial risk assessment in the tropical estuarine systems remain unresolved. The present study is the first approach of Next Generation Sequence (NGS) based viral metagenomic analysis of Cochin estuarine sediment. Viral particles were purified from 1.5 kg sediment samples collected from Cochin estuary, employing flocculation, and the purity was confirmed using epifluorescence microscopy. The flocculate was subjected to whole genome amplification using Illumina. Present NGS data provides information about the abundance of major bacteriophages, especially, cyanophages which play a significant role in ecosystem engineering and the biogeochemical cycle. In the present study, bacteriophages such as phages of Aeromonas, Bacillus, Salmonella, Vibrio, Burkholderia, Acanthocystis turfacea, Acidianus, Clostridium and Escherichia represented a major fraction. NGS result confirmed Aeromonas phages (19.78%) to be the most abundant communities present in the Cochin estuarine sediment. Cyanophages and phytoplankton attacking phage communities included A. turfacea virus, Chlorella virus, Acidianus filamentous virus, Ectocarpus siliculosus virus, Phaeocystis globosa virus, Chrysochromulina ericina virus, Emiliania huxleyi virus, Micromonas pusilla virus, Ostreococcus lucimarinus virus, Ostreococcus tauri virus, Synechococcus virus and Prochlorococcus virus. Unicellular photosynthetic Synechococcus and Prochlorococcus, abundant in oceans and estuaries, contribute to a substantial proportion of primary productivity, so the presence of these low-light adapted cyanobacteria attacking phages in estuarine sediments reveals that they are the key factor that controls the primary production and are also essential in preventing pathogenic bacterial population explosions. The data can be used as a road map for modelling efforts to link the role of viruses in determining carbon and nutrient availability in tropical estuarine ecosystems and the microbial risk assessment.