Novelty and uniqueness patterns of rare members of the soil biosphere

Journal Article · Tue Sep 30 04:00:00 EDT 2008 · Applied and Environmental Microbiology, 74(17):5422-5428

DOI:https://doi.org/10.1128/AEM.00410-08· OSTI ID:947902

Elshahed, Mostafa S; Youseff, Noha H; Spain, A M; Sheik, Cody; Najar, Fares Z; Sukharnikov, Leonid O; Roe, Bruce A; Davis, James P; schloss, Patrick D; Bailey, Vanessa L; Krumholz, Lee R

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 dataset 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%-37.1% of the total number of clones in the dataset 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 dataset, as well as members of multiple novel lineages within previously described phyla or candidate phyla), lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the dataset. While a fraction of the rare community was closely related to more abundant taxonomic groups in the dataset, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that recognizing these novelty and uniqueness patterns is key to understanding the origins, dynamics, and potential ecological roles of members of the soil’s rare biosphere.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 947902
• Report Number(s): PNNL-SA-60564; KP1208000
• Journal Information: Applied and Environmental Microbiology, 74(17):5422-5428, Journal Name: Applied and Environmental Microbiology, 74(17):5422-5428 Journal Issue: 17 Vol. 74; ISSN AEMIDF; ISSN 0099-2240
• Country of Publication: United States
• Language: English

Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
ABUNDANCE
BIOSPHERE
COMMUNITIES
DISTRIBUTION
GENES
GRAMINEAE
OKLAHOMA
SOILS