Deciphering the hidden role of soil viruses in nitrogen cycling revealed by metagenomic stable isotope probing

Viruses are the most abundant microbial entities on Earth, playing a critical role in elemental cycling. However, to date, there is no experimental evidence demonstrating whether viruses participate in nitrogen (N) cycling in soil. Here, we combined stable isotope probing (SIP) and metagenomics to detect 15N assimilation by viruses and their putative bacterial hosts in soil microcosms incubated with 15N-labeled N2. We recovered 609 viral operational taxonomic units (vOTUs, > 5 kb) and 49 metagenome–assembled genomes (MAGs) from the 15N-labeled soils using metagenomics. Based on metagenomic–SIP, a total of 65 vOTUs and 10 MAGs with potential N–transforming abilities were identified due to their exclusive enrichment in the heavy fractions under 15N2 treatment compared to 14N2, indicating their significance for soil N transformation. Moreover, three N–fixing MAGs (active diazotrophs) and one lytic virus with the potential to infect these diazotrophs were observed in the 15N-labeled soil. This indicates that viruses can assimilate 15N into their DNA via infection of diazotrophs. Additionally, two auxiliary metabolic genes associated with N cycling were identified in two viruses, suggesting that viruses may provision their hosts with N-cycling genes. Overall, our results demonstrate that soil viruses can promote microbial N turnover through viral lysis, highlighting the viral shunt as an important mechanism facilitating elemental cycling in soils.