Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts

Abstract

Background Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts’ metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments. Results Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders. Conclusions Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions.

Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

“…Interestingly, although individual AMG genes in the River Erpe were unique across compartments (27%), their functional categories were highly similar (69%) (Figure 6B). Our finding is different to a study recently reported form an estuary, where significant partitioning of AMG functions was reported between habitat types (water particle and sediment) (Luo et al, 2022). It is possible that due to the constant mixing of surface and HZ water in rivers, stratification at the genomic potential may be less notable, and expression information may be necessary to capture habitat specific differences.…”

The role of phages in proglacial stream biofilm communities characterized by microdiversity

“…Of the 953 bacterial MAGs with a predicted phage, particularly many phage-host interactions were identified involving MAGs classified as Rubrivirax (n=49), Novosphingobium (n=38), Rhizobacter (n=38), Aquabacterium (n=33) and Polaromonas (n=33)(Figure 3e). Similar to other work (Luo et al, 2022), the majority of phage-host interactions (84.2%) involved a single phage-host pair and only 6 phages had more than 10 predicted interactions with different MAGs (maxinteractions = 13). In line with generally high host specificity, vMAGs with multiple host interactions tended to interact with taxonomically similar MAGs (Figure 3e,f).…”

Enhanced Bacterium–Phage Symbiosis in Attached Microbial Aggregates on a Membrane Surface Facing Elevated Hydraulic Stress

“…Phages could compensate for bacterial adaptability and exhibited specific patterns in habitat patterns facing different environmental stresses. 93 The pAMGs related to energy metabolism might enhance nutrient utilization and thus fitness advantages for bacterial hosts in SMA. The pAMGs related to the biosynthesis of antioxidants could confer tolerance of bacterial hosts to oxidative stress in AMA (e.g., membrane cleaning chemicals).…”

“…Phages could compensate for bacterial adaptability and exhibited specific patterns in habitat patterns facing different environmental stresses . The pAMGs related to energy metabolism might enhance nutrient utilization and thus fitness advantages for bacterial hosts in SMA.…”