Functional metabolic annotations in the soil virosphere are rare but enriched for carbohydrate-active enzymes (CAZymes) and chitin decomposition functions
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Soil viruses are increasingly recognized as components of microbial communities that may alter how communities may function, yet the frequency and functional distribution of virus-encoded metabolic genes in soils remain poorly understood. Here, the Global Soil Virus Atlas gene catalog, comprising 1,432,147 viral genes from 1,223 soil samples across 13 ecosystem types, was analyzed to quantify the distribution of virus-encoded functional annotations and to estimate their representation in matched total metagenomic inventories. Functional annotations were assessed across KEGG Orthology, Pfam, and CAZy and grouped into carbon cycling, nitrogen cycling, and antibiotic resistance-associated categories. Only 1,903 viral genes (0.13%) had functional annotations. Carbon cycling dominated the annotated repertoire (1,840 genes; 96.5%), whereas nitrogen cycling (33 genes; 1.7%) and antibiotic resistance-associated functions (30 genes; 1.6%) were rare. Within carbon-cycling annotations, chitinase-associated genes were the most frequent named category (628 genes), followed by hemicellulase-associated functions. To estimate the representation of viral genes within broader metagenomic functional inventories, viral and total metagenomic annotations were compared across six exactly matched JGI studies. Viral contributions were usually low, with four of six studies showing less than 1% viral representation in targeted functions, but reached 9.86% for chitinase in one study. Together, these results show that virus-encoded metabolic genes are globally sparse in soils but are non-randomly concentrated in carbon-active CAZyme-linked functions, indicating that analyses restricted to microbial genes may underestimate predicted functional potential for selected degradation traits.
IMPORTANCE
Soil metagenomic studies usually interpret functional potential from microbial genes alone, even though soil viruses can also encode metabolic functions. In a global soil viral gene catalog, functionally annotated viral genes were rare overall, but the detectable signal was strongly concentrated in carbon-active CAZyme-linked functions, especially chitinase-associated annotations. Because viral diversity and activity can decouple from microbial responses to environmental gradients, virus-encoded functional genes may disproportionately affect gene-centric estimates of selected functions under stress or seasonal constraint (Zheng et al., 2022; Merges et al., 2023). A targeted comparison of viral and total metagenomic functional annotations further showed that viral contributions were usually small but could become non-trivial for selected carbon-degradation traits. These results identify viral CAZyme-associated functions as the clearest current case in which ignoring viruses may bias gene-centric estimates of predicted functional potential in soils. More broadly, the study provides a quantitative baseline for evaluating when virus-encoded genes are likely to matter for environmental metagenomic interpretation.
