Cyanophage host‐derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific

Abstract

Cyanophages encode host-derived genes that may increase their fitness. We examined the relative abundance of 18 host-derived cyanophages genes in metagenomes and viromes along depth profiles from the Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) where Prochlorococcus dominates a secondary chlorophyll maximum within the ODZ. Cyanophages at the oxic primary chlorophyll maximum encoded genes related to light and phosphate stress (psbA, psbD and pstS in T4-like and psbA in T7-like), but the proportion of cyanophage with these genes decreased with depth. The proportion of cyanophage with purine biosynthesis genes increased with depth in T4-like, but not T7-like cyanophages. No additional hostderived genes were found in deep T7-like cyanophages, suggesting that T4-like and T7-like cyanophages have different host-derived gene acquisition strategies, possibly linked to their different genome packaging mechanisms. In contrast to the ETNP, in the oxic North Atlantic T4-like cyanophages encoded psbA and pstS throughout the euphotic zone. Differences in pstS between the ETNP and the North Atlantic stations were consistent with differences in phosphate concentrations in those regimes. We suggest that the low proportion of cyanophage with psbA within the ODZ reflects the stably stratified low-light conditions occupied by their hosts, a Prochlorococcus ecotype endemic to ODZs.

Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean

“…As these waters are inhabited by hundreds of genomically diverse subpopulations of Prochlorococcus 50 , the broad host range of many T4-like cyanophages 18 , 19 , 22 , 51 may be advantageous for finding a suitable host. T4-like cyanophages also have a large and diverse repertoire of host-derived genes 21 , 51 —such as nutrient acquisition, photosynthesis and carbon-metabolism genes—that augment host metabolism 52 and may increase fitness in nutrient-poor conditions in the subtropics 51 . In contrast, T7-like clade A and B cyanophages seem to be better adapted to conditions in the transition zone (Fig.…”

Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation

“…For instance, viral psbA expression can sometimes account for over half of all psbA expression, highlighting the potential of viruses to directly affect important host metabolisms and biogeochemical cycles (Sieradzki et al, 2019). However, the relative abundance of psbA genes in T4-like cyanophages decreases with depth in the ETNP, which may be reflective of its low-light adapted Prochlorococcus host in anoxic chlorophyll maxima and suggests other AMGs are more important in OMZs (Fuchsman et al, 2021). For instance, several putative AMGs have been identified from the Cariaco Basin, the ETNP, the ETSP, and Saanich Inlet (Roux et al, 2014;Ahlgren et al, 2019;Mara et al, 2020;Vik et al, 2020;Gazitúa et al, 2021).…”

Virus-Host Interactions Reveal Potential Roles Towards Phosphorus Cycling in South Atlantic Ocean Euphotic Zones

“…MAGs from our study ranged from 0.6Mbp to 6.92Mbp and encoded between 854 to 6,648 proteins consistent with genome completeness estimates. Within bacterial MAGs, members of Bacteriodia (17), Gammaproteobacteria (26) and Alphaproteobacteria (14) classes were highly represented in each sampling station. For archaea, members of Thaumarchaeota (11) and Thermoplasmatota (5) phyla were only recovered from a few sampling sites (sampling stations 1, 2 and 3).…”

“…There has been some evidence showing the genetic potential of viruses to augment microbial metabolism through auxiliary metabolic genes (AMGs) [13][14][15][16][17]. AMGs encoded by marine bacteriophages are metabolically diverse and include various processes such as photosynthesis and the sequestration of nitrogen, sulphur, and carbon [18][19][20][21].…”