The air we breathe has more and more carbon dioxide in it over time. Carbon dioxide is a greenhouse gas, that contributes to global climate change. Other important greenhouse gasses are methane and nitrous oxide. The amount of these gasses that is emitted from or broken down in soil depends on organisms too small to see with the naked eye, like bacteria, that can emit these gasses as part of their respiration, or break them down to use as their food. Therefore, these microorganisms can increase or decrease the amount of greenhouse gasses in our air and atmosphere. The amounts of greenhouse gasses emitted from soil or broken down in soil can be measured, but if we want to be able to control these amounts - we have to know which microorganisms are responsible for emission or breakdown, and we cannot learn that by measuring amounts. We have to study the genetic material of these microorganisms, just like we decode the human genome, and determine which ones can break down greenhouse gasses and which ones can create and emit them. What makes this process more complicated, is that the amount of microorganisms in soil also depends on other organisms that can kill them, just like the amount of antelope in the savannah depends on the number of lions. Microorganisms can be killed by predators called protists, which are also microscopic, by other bacteria that eat bacteria, and by viruses. In fact, most of the viruses in our world only attack microorganisms, and cause no diseases in humans. Research done in the ocean teaches us that viruses can kill 20-50% of the microorganisms in water every day, and protists about the same. When a virus kills a microorganism, it causes it to explode and release organic material into the water, which is then turned into carbon dioxide that goes back into the atmosphere. Viruses in the ocean create about 20% of the carbon dioxide that is emitted from the ocean every day in this manner. In soil we don't know enough to estimate these numbers, and to identify how much predators affect the emission of greenhouse gasses. This is the topic of this project.
Using field soil incubated under controlled conditions, we were able to identify, for the first time, viruses that infect microorganisms that drive nitrogen and carbon cycling and particularly those that control emissions of nitrous oxide or methane from soil. This included the identification of a novel lineage of viruses infecting ammonia-oxidising archaea (see Figure 1). By following transfer of carbon from host to virus, we were able to demonstrate that these viruses are active in soil when their hosts are also active. I have developed this work to quantify amounts of methane carbon that flow through soil microorganisms into viruses.
In another part of the project, I studied a type of soil virus that is rarely studied. These viruses have genetic material made of RNA, like the corona virus, as opposed to DNA which is the type of genetic material humans have. We know that there are thousands of different types of these viruses in soil, and that they can infect and cause diseases in plants and in microorganisms. We demonstrated that soil RNA viruses, like DNA viruses, are also highly dynamic and respond to changing soil conditions and impact phosphorus availability, and essential soil nutrient (see Figure 2). The majority of hosts predicted for RNA viruses were bacteria and fungi and most soil bacteria are predicted to be infected by RNA bacteriophages within a week.
