Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.


While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.





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Publication Info

Brewer, Tess E, Emma L Aronson, Keshav Arogyaswamy, Sharon A Billings, Jon K Botthoff, Ashley N Campbell, Nicholas C Dove, Dawson Fairbanks, et al. (2019). Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons. mBio, 10(5). 10.1128/mbio.01318-19 Retrieved from

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Daniel D. Richter

Professor in the Division of Earth and Climate Science

Richter’s research and teaching links soils with ecosystems and the wider environment, most recently Earth scientists’ Critical Zone.  He focuses on how humanity is transforming Earth’s soils from natural to human-natural systems, specifically how land-uses alter soil processes and properties on time scales of decades, centuries, and millennia.  Richter's book, Understanding Soil Change (Cambridge University Press), co-authored with his former PhD student Daniel Markewitz (Professor at University of Georgia), explores a legacy of soil change across the Southern Piedmont of North America, from the acidic soils of primary hardwood forests that covered the region until 1800, through the marked transformations affected by long-cultivated cotton, to contemporary soils of rapidly growing and intensively managed pine forests.  Richter and colleagues work to expand the concept of soil as the full biogeochemical weathering system of the Earth’s crust, ie, the Earth’s belowground Critical Zone, which can be tens of meters deep.  The research examines decadal to millennial changes in the chemistry and cycling of soil C, N, P, Ca, K, Mg, and trace elements B, Fe, Mn, Cu, Be, Zr, and Zn across full soil profiles as deep at 30-m.  Since 1988, Richter has worked at and directed the Long-Term Calhoun Soil-Ecosystem Experiment (LTSE) in the Piedmont of South Carolina, a collaborative study with the USDA Forest Service that quantifies how soils form as natural bodies and are transformed by human action, and a study that has grown to become an international model for such long-term soil and ecosystem studies.  In 2005, Richter and students initiated the first comprehensive international inventory project of the world’s LTSEs, using an advanced-format website that has networked metadata from 250 LTSEs.  The LTSEs project has held three workshops at Duke University, NCSU's Center for Environmental Farming Systems, and the USDA Forest Service's Calhoun Experimental Forest and Coweeta Hydrologic Laboratory, hosting representatives from Africa, Asia, Australia, Europe, and the Americas.  Richter's 60-year old Long Term Calhoun Soil and Ecosystem Experiment is linked to similar experiments and platforms around the world via the ‘Long-Term Soil-Ecosystem Experiments Global Inventory’, assembled by Dan Richter, Pete Smith, and Mike Hofmockel."He is an active member of the International Commission on Stratigraphy’s Working Group on the Anthropocene.  Richter has written in the peer-reviewed literature about all of these projects, and in November 2014 his soils research at the Calhoun and his soils teaching were featured in Science magazine.

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