Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

Abstract

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus–host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.DOI: http://dx.doi.org/10.7554/eLife.03125.001

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

“…Four AMGs (i.e. similar to a domain from the "metabolism" category) were then selected for further study because of their central role in sulfur (dsrC and soxYZ) or nitrogen (P-II, amoC) cycle, and the fact that these had never been detected in a surface ocean viral genome so far (dsrC/tusE-like genes have been detected in deep water viruses 14,29 ). To evaluate if an AMG was "known", a list of PFAM domain detected in NCBI RefSeqVirus and Environmental Phages was computed based on a similar hmmsearch comparison (threshold of 40 on bit score and 0.001 on e-value), and augmented by manual annotation of AMGs from 24,82 .…”

“…Conserved residues are indicated below the alignment, and the two conserved C residues representing the active sites of "true dsrC" (Cys-B and Cys-A) are named as in 33 . Viral AMGs are highlighted in bold, with previously described anoxic SUP05 viruses sequences in red (from 14,29 ) and epipelagic GOV sequences in black. …”

“…Here we focus specifically on 4 AMGs (dsrC, soxYZ, P-II and amoC, see Extended Data Table 1) because of their critical roles in sulfur or nitrogen cycling and their novelty in epipelagic ocean viruses. Three of these are not yet known in viruses, and one, dsrC-like genes, has been observed in viruses, but only from anoxic deep-sea environments 14,29 .…”

Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

“…They were also limited on explaining how each of these components, in turn, influence biomass production of heterotrophic bacteria and shape the carbon flux in food webs (Azam et al, 1994). Small flagellates were seen as key players bacteria mortality but, as knowledge increased, it become evident that virus infection contributed significantly to bacterial loss (Bergh et al, 1989;Bratbak et al, 1990;Fuhrman and Noble, 1995;Petersen and Dubilier, 2014;Roux et al, 2014). The overwhelming evidences pointing to virus-induced mortality of bacteria, has noted by Fenchel (2008), made them new players in the microbial loop.…”

Comparative study of viromes from freshwater samples of the Ile-Balkhash region of Kazakhstan captured through metagenomic analysis

“…The length of the obtained sequences ranged from 162 to 190,000 bp. The contigs were then uploaded to Metavir (http://metavir-meb.univ-bpclermont.fr/) pipeline for phylogenetic analysis (N 151,301, 173,141, 116,319) [14]. Sequences were also uploaded and analyzed using MG-RAST server (http://metagenomics.anl.gov/), an online metagenome annotation pipeline [15].…”