Underexplored viral auxiliary metabolic genes in soil: Diversity and eco‐evolutionary significance

Abstract

Bacterial viruses are the most abundant biological entities in soil ecosystems. Owing to the advent of metagenomics and viromics approaches, an ever‐increasing diversity of virus‐encoded auxiliary metabolic genes (AMGs) have been identified in soils, including those involved in the transformation of carbon, phosphorus, and sulfur, degradation of organic pollutants, and antibiotic resistance, among other processes. These viral AMGs can alter soil biogeochemical processes and metabolic activities by interfering with bacterial host metabolism. It is recognized that viral AMGs compensate for host bacterial metabolism outputs by encoding accessory functional genes and are favourable for the hosts' adaptation to stressed soil environments. The eco‐evolutionary mechanisms behind this fascinating diversity of viral AMGs in soil microbiomes have begun to emerge, such as horizontal gene transfer, lytic‐lysogenic conversion, and single‐nucleotide polymorphisms. In this mini‐review, we summarize recent advances in the diversity and function of virus‐encoded AMGs in the soil environment, especially focusing on the evolutionary significance of AMGs involved in virus‐host interactions. This mini‐review also sheds light on the existing gaps and future perspectives that could have major significance for viral AMGs research in soils.

Novel phages of Pseudomonas syringae unveil numerous potential auxiliary metabolic genes

“…In summary, 8 out of 25 phages (32%) have potential AMGs present in their genome. It should be noted that there is currently a lack of a database and pipeline to annotate and identify AMGs in a robust and reliable manner [28]. Future research could aim to validate the function of these particular genes in the laboratory.…”

Viral AMGs‐driven pentose phosphate pathway in natural wetland

“…When focusing on lifestyle-specific viruses, AMGs encoded by both lytic and temperate viruses are habitatdependent and host-specific [45]. AMGs are host-specific to some extent, and studies have shown that viral AMGs can be acquired and maintained from their hosts [46,47].…”

The role of rhizosphere phages in soil health

“…In addition to facilitating horizontal gene transfer, temperate phages are also capable of altering host metabolism through the expression of AMGs (Yu et al 2015 , Sun et al 2023a ) (Fig. 1D ).…”

“…In cyanophages, AMGs have been associated with functions such as photosynthesis, nucleic acid synthesis, metabolism, and stress tolerance (Thompson et al 2011 , Kelly et al 2013 , Enav et al 2014 ). Soil environments are also important reservoirs for viruses that encode AMGs (Sun et al 2023a ). Phages can also provide their host bacteria beneficial traits through lysogenic conversion where they integrate into bacterial chromosome as prophages.…”