focus: Soils

Soil Research in the Sullivan Lab

Terrestrial ecosystems represent the near-opposite conditions as those in the oceans with drastic spatio-temporal changes in nutrient availability, extensively structured habitats, and extremely steep redox gradients. Yet, just as in the oceans, it is becoming clear that microbes also play critical, if not central roles in soils. Our group now studies viruses that infect soil microbes along a climate change chrono-sequence in thawing permafrosts, as well as wet-up events in diverse grassland soils. Soils, however, are extremely challenging as their micro-heterogeneity and chemical variability preclude universally optimal viral particle capture approaches, which has led us to lean more upon mining viral signals from microbial datasets (metagenomic, metatranscriptomic, metaproteomic) than relying as heavily upon viral fraction metagenomes (viromes). Collaboratively, this work is contextualized by intensive geochemical measurements of fluxes and nutrient flow, which represent some of the few measurements not yet available in marine systems.

Beyond viral ecogenomics Qs (see “oceans”), soil-specific key research Qs include:
– Are soil viruses and viral communities fundamentally different to those in the oceans?
– How do soil viruses respond to changing ecological conditions?
– What fraction of carbon flows through viruses?

As in our oceans research, we collaborate with diverse microbial ecology and biogeochemistry labs to maximize our understanding of viral roles in soil ecosystems. These collaborations include the IsoGenie Consortium for the permafrost soils work and researchers at LLNL and UC Berkeley for the grassland soils work. Our current work is focused on developing a baseline understanding of the taxonomic identities and ecological impacts of DNA viruses in these soils systems. This work is funded by the DOE.

We are also a part of the phytobiomes alliance, a collaboration between industry and academia with the goal of building a phytobiome-based foundation for accelerating the sustainable production of food, feed, and fiber.






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Recent publications in soil research
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Soil Research Feature

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Recent Soil Publications

  • Trubl, G., Roux, S., Solonenko, N., Li, Y., Bolduc, B., Rodriguez-Ramos, J., Eloe-Fadrosh, E.A., Rich, V., & Sullivan, M.B. 2019. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. PeerJ. 7:e7265.  LINK PDF
  • Wilpiszeski, R., Aufrecht, J., Retterer, S., Sullivan, M.B., Graham, D., Pierce, E., Zablocki, O., Palumbo, A., & Elias, D. 2019. Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales. Applied and Environmental Microbiology. 85(14):e00324. LINK PDF
  • Daly, R., Roux, S., Borton, M., Morgan, D., Johnston, M., Booker, A., Hoyt, D., Meulia, T., Wolfe, R., Hanson, A., Mouser, P., Moore, J., Wunch, K., Sullivan, M.B., Wrighton, K. & Wilkins, M. 2019. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nature Microbiology. 4: 352-361.  LINK  PDF

Soil Researchers

Field Work in Soils Research


One third of the world’s carbon is held in permafrost soils; however, due to warmer temperatures, many permafrost regions have begun to thaw causing massive amounts of organic material become available to microbes, which metabolize the nutrients and release carbon dioxide and methane (both greenhouse gases). Understanding this process is a challenge due to the complexity of carbon dynamics. Scientists at the University of Arizona (Dr. Virgina Rich, Dr. Scott Saleska, and Dr. Matt Sullivan) have teamed with scientists at the University of Queensland in Australia, University of Stockholm in Sweden, and Florida State University to understand this important environmental system. Sampling and measurements are being collected from Stordalen Mire in Abisko National Park in Sweden, just north of the Arctic Circle. A key challenge of this work is to integrate ecosystem-scale measurements with molecular-scale studies of microorganisms and viruses.

UANews article, Sept. 23, 2013: How Soil Microbes Affect Global Climate