Metagenomic stable isotope probing reveals bacteriophage participation in soil carbon cycling

Soil viruses are important components of the carbon (C) cycle, yet we still know little about viral ecology in soils. We added diverse ¹³ C-labelled carbon sources to soil and we used metagenomic-SIP to detect ¹³ C assimilation by viruses and their putative bacterial hosts. These data allowed us to link a ¹³ C-labelled bacteriophage to its ¹³ C-labelled Streptomyces putative host, and we used qPCR to track the dynamics of the putative host and phage in response to C inputs. Following C addition, putative host numbers increased rapidly for 3 days, and then more gradually, reaching maximal abundance on Day 6. Viral abundance and virus:host ratio increased dramatically over 6 days, and remained high thereafter (8.42 ± 2.94). From Days 6 to 30, virus:host ratio remained high, while putative host numbers declined more than 50%. Putative host populations were ¹³ C-labelled on Days 3-30, while ¹³ C-labelling of phage was detected on Days 14 and 30. This dynamic suggests rapid growth and ¹³ C-labelling of the host fueled by new C inputs, followed by extensive host mortality driven by phage lysis. These findings indicate that the viral shunt promotes microbial turnover in soil following new C inputs, thereby altering microbial community dynamics, and facilitating soil organic matter production.