Abstract
Bacteroidetes is one of the most abundant heterotrophic bacterial taxa in the ocean and play crucial roles in recycling phytoplankton-derived organic matter. Viruses of Bacteroidetes are also expected to have an important role in the regulation of host communities. However, knowledge on marine Bacteroidetes viruses is biased toward cultured viruses from a few species, mainly fish pathogens or Bacteroidetes not abundant in marine environments. In this study, we investigated the recently reported 1,811 marine viral genomes to identify putative Bacteroidetes viruses using various in silico host prediction techniques. Notably, we used microbial metagenome-assembled genomes (MAGs) to augment the marine Bacteroidetes reference genomic data. The examined viral genomes and MAGs were derived from simultaneously collected samples. Using nucleotide sequence similarity-based host prediction methods, we detected 31 putative Bacteroidetes viral genomes. The MAG-based method substantially enhanced the predictions (26 viruses) when compared with the method that is solely based on the reference genomes from NCBI RefSeq (7 viruses). Previously unrecognized genus-level groups of Bacteroidetes viruses were detected only by the MAG-based method. We also developed a host prediction method based on the proportion of Bacteroidetes homologs in viral genomes, which detected 321 putative Bacteroidetes virus genomes including 81 that were newly recognized as Bacteroidetes virus genomes. The majority of putative Bacteroidetes viruses were detected based on the proportion of Bacteroidetes homologs in both RefSeq and MAGs; however, some were detected in only one of the two datasets. Putative Bacteroidetes virus lineages included not only relatives of known viruses but also those phylogenetically distant from the cultured viruses, such as marine Far-T4 like viruses known to be widespread in aquatic environments. Our MAG and protein homology-based host prediction approaches enhanced the existing knowledge on the diversity of Bacteroidetes viruses and their potential interaction with their hosts in marine environments.
Highlights
Marine heterotrophic prokaryotes are responsible for processing almost half of the organic matter that is fixed by marine phytoplankton, playing an important role in the global carbon cycle (Azam and Malfatti, 2007)
To identify novel Bacteroidetes-virus pairs, we first conducted host prediction analyses on the 1,811 environmental viral genomes (EVGs) based on CRISPR spacer sequences, tRNA genes, sequence similarity (BLASTn) and Oligonucleotide frequency (ONF) distance, by using 3,695 Bacteroidetes genomes in NCBI RefSeq and 518 Bacteroidetes-metagenome-assembled genomes (MAGs) (Table 1)
Microbial MAGs have advantages in the computational detection of uncultured marine Bacteroidetes viruses compared with the microbial genomes in the current public databases
Summary
Marine heterotrophic prokaryotes are responsible for processing almost half of the organic matter that is fixed by marine phytoplankton, playing an important role in the global carbon cycle (Azam and Malfatti, 2007). Bacteroidetes inhabit various marine environments ranging from coastal water to open ocean habitats (Alonso et al, 2007; Pommier et al, 2007). They are especially abundant during and after the phytoplankton blooms and believed to have an important role in the decomposition and remineralization of the phytoplankton biomass (Teeling et al, 2012). Despite being the abundant species during phytoplankton blooms, isolated marine Bacteroidetes strains are rarely observed in environment; most abundant lineages of marine Bacteroidetes remain poorly characterized (Unfried et al, 2018)
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