Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.
Abstract
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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https://hdl.handle.net/10161/21223Published Version (Please cite this version)
10.1128/mbio.01318-19Publication Info
Brewer, Tess E; Aronson, Emma L; Arogyaswamy, Keshav; Billings, Sharon A; Botthoff,
Jon K; Campbell, Ashley N; ... Fierer, Noah (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 https://hdl.handle.net/10161/21223.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
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

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