Periodic Reporting for period 1 - DIVOBIS (Determining Impact of Viruses on Biogeochemical processes In Soil)
Periodo di rendicontazione: 2022-09-01 al 2024-08-31
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.
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.
1. We characterised viruses having infected autotrophic ammonia-oxidising archaea (AOA) in two nitrifying soils of contrasting pH by following transfer of assimilated CO2-derived 13C from host to virus via DNA stable-isotope probing and metagenomic analysis. Using DNA stable-isotope probing we developed a novel hybrid analysis approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of 13C isotopically enriched high buoyant density DNA reads to identify activity of AOA. We identified, for teh first time, viruses of AOA and were able to characterise their lifestyle with the majority predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase genes suggesting infection may augment copper uptake essential for central metabolic functioning of their hosts. These findings indicate virus infection of AOA may be a frequent process during nitrification in soil with potential to influence host physiology and activity. This work was published in the ISME Journal (2023).
2. RNA virus data was acquired from a 3 weeks long replicated time series after soil rewetting with or without phosphorus addition. 11,370 species level genome of RNA viruses were identified, representing all three structural types of rNA viruses: double stranded RNA, positive sense single stranded RNA and negative sense since stranded RNA. On average, about 50% of these viruses likely infect fungi, 25% infect bacteria and the rest are mostly plant viruses. Temporal dynamics vary significantly by viral phylum and by addition of P. With P addition: fungal viruses start at a median abundance on the order of 100 reads per kilo million (RPKM) and drop to 0 after 1-2 weeks, phages also have median low abundance and peak briefly at circa 30 RPKM after 1 week. While the abundance of each viral species of these clades is low, their diversity is extremely high and adds up to the high aggregated relative abundance. These are all positive sense RNA viruses. Less abundant in total but also less diverse plant and insect viruses have higher abundance per virus. Most of these phyla decrease in abundance over time except for Tombusviridae (plant viruses) which become abundant only after a week and drop back to zero median abundance at 3 weeks. The most abundant (per virus) are Kitrinoviricota, on the order of 1000 RPKM, which are generally eukaryotic viruses. Without P addition some phyla disappear completely, like Qinviridae and Zhaoviridae, whereas others appear, such as Hypoviridae and Picornaviridae. A manuscript describing this work has recently been submitted to Soil Biology and Biochemistry, also made publicly available on bioRxiv.
3. We established soil microcosms incubated with 12CH4 or 13CH4 to stimulate methane oxidising (methanotroph) activity for both host and viruses. For both series of microcosms, functional process rates were measured (nitrification or methane oxidation/CO2 production). DNA-SIP experiments were successfully performed for all microcosms and we successfully enriched and characterised methanotroph hosts and viruses whose abundance and activity correlated with functional processes. This work is not yet complete and undergoing analysis. We anticipate submission of a paper mid-2025.
2. RNA virus data was acquired from a 3 weeks long replicated time series after soil rewetting with or without phosphorus addition. 11,370 species level genome of RNA viruses were identified, representing all three structural types of rNA viruses: double stranded RNA, positive sense single stranded RNA and negative sense since stranded RNA. On average, about 50% of these viruses likely infect fungi, 25% infect bacteria and the rest are mostly plant viruses. Temporal dynamics vary significantly by viral phylum and by addition of P. With P addition: fungal viruses start at a median abundance on the order of 100 reads per kilo million (RPKM) and drop to 0 after 1-2 weeks, phages also have median low abundance and peak briefly at circa 30 RPKM after 1 week. While the abundance of each viral species of these clades is low, their diversity is extremely high and adds up to the high aggregated relative abundance. These are all positive sense RNA viruses. Less abundant in total but also less diverse plant and insect viruses have higher abundance per virus. Most of these phyla decrease in abundance over time except for Tombusviridae (plant viruses) which become abundant only after a week and drop back to zero median abundance at 3 weeks. The most abundant (per virus) are Kitrinoviricota, on the order of 1000 RPKM, which are generally eukaryotic viruses. Without P addition some phyla disappear completely, like Qinviridae and Zhaoviridae, whereas others appear, such as Hypoviridae and Picornaviridae. A manuscript describing this work has recently been submitted to Soil Biology and Biochemistry, also made publicly available on bioRxiv.
3. We established soil microcosms incubated with 12CH4 or 13CH4 to stimulate methane oxidising (methanotroph) activity for both host and viruses. For both series of microcosms, functional process rates were measured (nitrification or methane oxidation/CO2 production). DNA-SIP experiments were successfully performed for all microcosms and we successfully enriched and characterised methanotroph hosts and viruses whose abundance and activity correlated with functional processes. This work is not yet complete and undergoing analysis. We anticipate submission of a paper mid-2025.
The research programme was fundamental research. All outcomes advancing beyond the current state-of-the-art are new knowledge on soil virus ecology.