Research topics

My research interests focus on the role of microbiomes, specifically viruses in the ecology and evolution of host cells and ecosystems, and I am particularly interested in exploring the following topics and questions:

Highlight from recent research: Significance of soil virus in understanding climate change

Study Overview: Our study investigated the virus community in a thawing permafrost system (Stordalen Mire, within an Arctic Circle in Northern Sweden) over seven years using metagenomic data. The research aimed to understand how global warming impacts the diversity, dynamics, and ecological roles of viruses in permafrost soils, and how these changes might influence the broader ecosystem, particularly carbon cycling.

Key Findings:

1. High novelty and diversity of soil viruses

• The study identified 5051 virus operational taxonomic units (vOTUs), effectively doubling the number of known viruses for the Stordalen Mire site.

• Most of these viruses were novel at the species level, with over 99% being unique compared to existing databases.

• Despite extensive study, the diversity of viruses in permafrost remains largely uncaptured, indicating a vast, unexplored viral reservoir in these environments.

2. Habitat-specific and ephemeral virus communities

• Virus communities were found to be largely specific to particular habitats (palsa, bog, fen) within the thaw gradient, with minimal overlap between different habitats.

• Many vOTUs were ephemeral, present only in specific years, suggesting a high turnover rate of viruses in these environments.

3. Limited long-term temporal changes

While virus communities varied significantly across different habitats and depths, there was no consistent, long-term change in viral diversity or abundance ratios over the seven-year period.

4. Linkages to carbon cycling

• The study predicted that several viruses were linked to microbial lineages involved in carbon cycling processes, such as methanotrophy and methanogenesis. This includes viruses infecting Candidatus Methanoflorens, a major methane producer.

• The presence of virus-encoded auxiliary metabolic genes (AMGs), including those involved in carbon degradation, suggests that viruses could play a role in influencing carbon cycling in thawing permafrost.

5. Environmental factors and virus community dynamics

The study found correlations between virus community structures and environmental factors such as methane concentrations, bulk density, and oxygen levels, indicating that these factors might influence viral ecology in permafrost environments.

Significance of the research

This study contributes to our understanding of soil viruses, particularly in the context of climate change. The discovery of a high number of novel viruses and their potential roles in carbon cycling underscores the importance of viruses in permafrost ecosystems. Given the role of permafrost in storing carbon, understanding how thawing affects microbial and viral communities is crucial. This knowledge is vital as these changes could influence the release of greenhouse gases, potentially accelerating climate change.

Implications for future research

1. Focus on long-term virus dynamics

Future studies should continue monitoring virus communities over longer periods to determine if the observed high turnover and habitat specificity persist and how they might impact ecosystem processes.

2. Explore virus-host interactions

Understanding the interactions between viruses and key microbial hosts involved in carbon cycling should be a priority. This includes further exploring virus-encoded AMGs and their direct impact on microbial metabolism. Additionally, employing an experimental approach such as Hi-C could enhance the prediction of virus-host interactions, providing a more detailed understanding of these complex relationships.

3. Investigate the impact of environmental changes

Research should focus on how specific environmental changes, such as increased temperatures and shifts in moisture levels, directly influence virus communities and their ecological functions. Importantly, incorporating viral data into climate change models could lead to a more comprehensive understanding of the impact of climate on microorganisms and vice versa. This modelling approach could improve predictions of climate change and inform mitigation strategies.

4. Expand viral discovery

The study highlights the vast unknown diversity of viruses in soil systems, suggesting that more extensive sampling and improved methodologies could reveal even more about the roles these viruses play in terrestrial ecosystems. There is also a need to expand the exploration of the virosphere, including RNA viruses, ssDNA viruses, giant viruses, and virophages, which remain understudied. This expansion could provide critical insights into a more holistic investigation of soil viruses and their ecological roles and impact on climate-relevant processes.

This research provides a crucial foundation for understanding how viruses might influence climate-relevant processes in a warming world and sets the stage for future investigations into the complex interactions between viruses, microbes, and the environment.

See the publication: Sun & Pratama et al (2024). Environ. Microbiol. 26(8): e16665

Virus community ecology

Viruses are the most abundant entities on the planet, playing a crucial role in ecosystems by controlling host mortality, acting as agents of horizontal gene transfer, and reprogramming host metabolisms. My research focuses on utilizing multiomics and innovative bioinformatics tools to explore the diversity, abundance, and ecological roles of virus communities (viromes) across various biomes, with a particular emphasis on terrestrial ecosystems. The research questions I aim to address include: 1) What is the abundance and diversity of virome across different ecosystems? 2) How does the presence and distribution of viromes impact the diversity and diversification of microbiome? 3) What are the key interactions between viruses and their microbial hosts that drive ecosystem processes and functions? 4) How do environmental factors influence the dynamics and evolution of viromes in terrestrial habitats? Through this work, I seek to uncover the complex interactions and ecological significance of viruses in shaping microbial communities and ecosystem health.

Virus-host coevolution

Soil is often described as a desert for microbes due to its generally complex and heterogeneous conditions. However, soil hotspots, such as the rhizosphere (the region around plant roots) and the mycosphere (the area around fungal hyphae), are exceptions, teeming with a high abundance and activity of microbiomes. These hotspots not only support diverse microbial communities but also foster high rates of horizontal gene transfer (HGT), a key mechanism for microbial evolution and adaptation. The research questions I aim to address include: 1) How do different soil hotspots exhibit varying rates of HGT and the presence of mobile genetic elements? 2) Is there selection pressure that drives the occurrence of HGT in these environments? 3) Which mobile elements are the most prevalent agents of HGT in these distinct hotspots? 4) What are the consequences of HGT on the evolutionary dynamics and coevolution of microbiomes within these hotspots? 5) What specific functions are being transferred through HGT, and how do these transfers impact the functionality and resilience of microbial communities? Through these questions, I aim to uncover the mechanisms that drive microbial interactions and evolution in soil ecosystems.

Virus impacts on global warming

Global warming is a pressing issue that threatens the stability of our planet's ecosystems. Soil, which sequesters three times the amount of carbon currently in the atmosphere, plays a crucial role in regulating this balance. However, global warming poses a significant threat to the release of this stored soil carbon, potentially accelerating the climate crisis. Microbial activity in the soil creates a positive feedback loop that further amplifies global warming, yet our limited understanding of soil viral activity hinders a complete understanding of how viruses contribute to these cycles. The research questions I aim to address include: 1) To what extent do viruses affect or contribute to global climate change? 2) Through what mechanisms do viruses influence the carbon cycle and microbial activity in the soil, thus global warming? 3) Does the impact of viruses on global warming differ across various soil biomes? 4) How do viruses modulate the interactions between microbial communities and their environment in the context of climate change? 5) What are the potential feedback loops involving viruses that could exacerbate or mitigate global warming? 6) How might changes in viral populations and activities respond to or drive shifts in climate conditions over time? 7) Can we utilize soil viruses as a tool to mitigate global warming by influencing microbial processes and carbon storage? Through these investigations, I seek to illuminate the hidden roles that viruses play in the complex dynamics of global climate change and explore innovative strategies to address this global challenge.