Novelty and uniqueness patterns of rare members of the soil biosphere

Abstract

Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.

FIG. 1.

Kessler Farm soil overall library composition. (A) Distribution of various phyla in KFS. (B) Species distribution pattern of KFS OTU_0.03 asignments. (C) Rarefaction curve at different taxonomic cutoffs.

FIG. 2.

(A) Correlation between novelty and abundance of clones within each OTU_0.03 identified in the KFS data set. (B) Correlation between average percent sequence divergence and abundance of clones within KFS OTU_0.03 assignments.

FIG. 3.

Distance NJ tree highlighting the phylogenetic position of five novel candidate phyla identified in KFS data set. The tree was constructed from 1,643 aligned sequences using the ARB-NJ method with Olsen correction and a Lane mask filter. Bootstrap values are based on 1,000 replicates and are shown for novel candidate phyla branches.

FIG. 4.

Quantification of the proportion of unique clones within the KFS rare biosphere. Rare OTUs are defined at two cutoffs: those containing a single clone (n = 1) and those containing five or fewer clones (n ≤ 5). (A) Percentage of clones belonging to rare OTUs at different taxonomic cutoffs expressed as a fraction of the total number of clones in the KFS data set (13,001). (B) Percentage of clones belonging to rare OTUs at different taxonomic cutoffs expressed as a fraction of the number of clones belonging to rare OTUs at a 97% taxonomic cutoff (OTU_0.03).