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.

Keywords: critical zone; metagenomics; microbial ecology; microbial traits; soil microbiology.

FIG 1

(A) Site map of sampling locations. We analyzed bacterial and archaeal communities from two soil profiles located at each of 10 different CZOs across the United States. Each profile was sampled in 10-cm intervals from surface soils to 1 m in depth (where possible). (B) Bray-Curtis dissimilarity to surface samples increases with depth. As depth increases, soil bacterial and archaeal communities become less similar to those communities at the surface. (C) Bacterial and archaeal diversity generally decreases with depth. Colors of points match the colors of the CZO sites indicated in panel A with two profiles sampled per site (n = 20). (D) The proportion of 16S rRNA gene sequences from the sampled soils for which representative genome data are available decreases with depth. We matched our 16S rRNA gene amplicon sequences to 16S rRNA genes from finished bacterial and archaeal genomes in the NCBI database. At deeper soil depths, we found that fewer taxa in our data set had matches to publicly available genomes, indicating that the bacterial and archaeal taxa found in deeper soil horizons are less represented in genomic databases than those found in surface soils. More details on these analyses are presented in Materials and Methods. The purple trend lines represent smoothed conditional means, generated using the loess modeling method.

FIG 2

Different soil profiles have distinct microbial communities. Here, we show the relative abundances of the eight most abundant phyla identified from our 16S rRNA gene amplicon data. Not all profiles were sampled to 1 m due to variable bedrock depth. Note that the two profiles sampled from each CZO site were selected to represent distinct soil types (details on soil characteristics are available in Data Set S1 in the supplemental material).

FIG 3

Five bacterial and archaeal phyla that consistently increased in relative abundance with soil depth. These phyla were identified via Spearman rank correlations against depth (FDR-corrected P values < 0.02, rho > 0.22). The purple trend lines represent smoothed conditional means, generated using the loess modeling method. For details on all phylum level abundances in each individual soil profile, see Table S5.

FIG 4

(A) The 16S rRNA gene relative abundance of phylum Dormibacteraeota is variable across different soil profiles but generally increases with depth. The samples used for the Dormibacteraeota genome assemblies are noted with stars. The trend lines represent smoothed conditional means, generated using the loess modeling method. (B) The two Dormibacteraeota genomes we assembled from soil profile metagenomic data cluster phylogenetically with previously published Dormibacteraeota genomes. Our deep soil genomes also fall near the known sister phyla Chloroflexi and Armatimonadetes, validating their identity as members of candidate phylum Dormibacteraeota. This tree was created using the concatenated marker gene phylogeny generated from GTDBTk (26) and was plotted using iTOL (70). Only closely related phyla are included in the tree. Genomes assembled in this study are indicated in red, and all other AD3/Dormibacteraeota genomes originated from either reference or . The family groupings for the Dormibacteraeota tree were first presented in reference .