Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone

Abstract

Viruses interfere with their host’s metabolism through the expression of auxiliary metabolic genes (AMGs) that, until now, are mostly studied under large physicochemical gradients. Here, we focus on coastal marine ecosystems and we sequence the viral metagenome (virome) of samples with discrete levels of human-driven disturbances. We aim to describe the relevance of viromics with respect to ecological quality status, defined by the classic seawater trophic index (TRIX). Neither viral (family level) nor bacterial (family level, based on 16S rRNA sequencing) community structure correlated with TRIX. AMGs involved in the Calvin and tricarboxylic acid cycles were found at stations with poor ecological quality, supporting viral lysis by modifying the host’s energy supply. AMGs involved in “non-traditional” energy-production pathways (3HP, sulfur oxidation) were found irrespective of ecological quality, highlighting the importance of recognizing the prevalent metabolic paths and their intermediate byproducts. Various AMGs explained the variability between stations with poor vs. good ecological quality. Our study confirms the pivotal role of the virome content in ecosystem functioning, acting as a “pool” of available functions that may be transferred to the hosts. Further, it suggests that AMGs could be used as an ultra-sensitive metric of energy-production pathways with relevance in the vulnerable coastal zone and its ecological quality.

Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus

“…The marine MVGs were extracted from the IMG/VR database v3 ( Roux et al, 2021 ), Pearl River estuary database ( Xu et al, 2022 ), Red Sea database ( Hevroni et al, 2020 ), sequences assembled from 14 coastal stations ( Tsiola et al, 2020 ), sequences assembled from the 78 marine viromes ( Coutinho et al, 2017 ), MedDCM fosmid library ( Mizuno et al, 2013 ), Station ALOHA assembly free virus genomes ( Beaulaurier et al, 2020 ), and ALOHA 2.0 viromic database ( Luo et al, 2020 ). In order to recruit MVGs closely related to CRP-901 and CRP-902, the protein sequences of the four conserved genes of CRP-901 and CRP-902 were aligned using MUSCLE, including bifunctional DNA primase-polymerase, DNA helicase, capsid, and terminase large subunit (TerL).…”

Penyediaan Air Bersih di Era Tatanan Normal Baru

“…Such conditions can inhibit the coronavirus by destroying the fat component of its envelope that was leading to its detachment from surfaces. However, many pathogenic viruses that usually infect aquatic life exist in seawater (Aguilera-Rivera et al 2019;Leiva-Rebollo et al 2020;Liu et al 2020;Nabi and Khan 2020;Tsiola et al 2020). Marine viruses are the most abundant life form in the sea, they can infect the phytoplankton whale, and marine viruses can also spread to terrestrial mammals (Suttle 2005(Suttle , 2007.…”

Genetic diversity of virus auxiliary metabolism genes associated with phosphorus metabolism in Napahai plateau wetland

“…For example, genes involved in the electron transfer ( psaA , petE , petF , ptoX , speD , hli ) and light-harvesting processes ( ho1 , pcyA , pebS , cpeT ), infected phage AMGs carrying photosynthetic system genes complements photosynthetic electron transport while transferring energy from the carbon fixation to the pentose phosphate pathway, leading to the increase of viral lysis 5 , 6 . Tsiola et al conducted a metavirome study on coastal surface waters in the Ionian and South Aegean Seas, and revealed that viral AMGs participated in non-traditional energy production pathways (3HP, sulfur oxidation), Calvin cycle and TCA cycle 7 . Another class of AMGs does not usually appear in the KEGG pathway and encoded only proteins with general, unspecified metabolic roles or peripheral proteins involved in assembly and membrane transport functions.…”