Unearthing the hidden world of soil viruses

By Dr. Janet K. Jansson, Chief Scientist & Laboratory Fellow, Biological Sciences Division, Pacific Northwest National Laboratory

Soil is a rich habitat for microbial life. A highly diverse community of soil microbes are responsible for many of the functions that are linked to soil health, including soil nutrient cycling and support of plant growth. Although we are gaining an increasing understanding of how different cellular microorganisms, such as bacteria and fungi, contribute toward vital functions in the soil environment, the functions carried out by soil viruses remain largely an enigma. This knowledge gap is disconcerting considering that soil viruses are key regulators of microbial populations in all of Earth’s habitats, from oceans to humans. The reason that we know so little about soil viruses is that they are hard to study in the complex soil environment. Free viruses often absorb to soil particles and are hard to extract. Some other viruses that target bacteria, or bacteriophage (phage), may hide within the bacterial host genome. This life strategy is known as lysogeny and the phage are known as temperate phage.  Fortunately, new tools, such as whole genome sequencing (metagenomics) are beginning to uncover the identities of soil viruses. Many soil viruses found in soil metagenomes are novel and unlike anything previously described.

Soil viruses are influenced by historical amounts of precipitation as shown by comparing viral types in historically dry, to irrigated, to historically wet soils

(Wu et al., 2021: https://doi.org/10.1128/mBio.02595-21)

Interestingly, differences in the soil environment, such as a change in soil moisture, can influence the types of viruses and their life strategies. For example, recent research suggests that as soil becomes drier, as is expected to happen in many soils due to climate change, there is a transition of soil phage to be lysogenic instead of lysing their hosts. This shift in viral life strategy has implications in how soil bacterial populations are regulated by viruses. By contrast, when soils are wetter, such as in areas with increasing amounts of precipitation, many soil viruses become lytic and kill their bacterial hosts. The process of lysing of bacterial cells releases their cellular contents back into the soil habitat. These dead cell contents can be recycled by other microorganisms – a process known as the viral shunt. The viral shunt keeps the microbial nutrients within the microbial food web, instead of allowing the nutrients to be consumed by higher organisms such as protozoa, worms and plants. How the viral shunt impacts the soil carbon cycle is an exciting area of current research. Our recent publication summarizes current knowledge about soil viral diversity and how soil viruses can potentially be impacted by climate change.

Reference:

Jansson, J.K., Wu, R. Soil viral diversity, ecology and climate change. Nat Rev Microbiol (2022). https://doi.org/10.1038/s41579-022-00811-z