Original Article

Subject Category: Microbial ecology and functional diversity of natural habitats

The ISME Journal (2009) 3, 992–1000; doi:10.1038/ismej.2009.43; published online 30 April 2009

Abundance, composition, diversity and novelty of soil Proteobacteria

Anne M Spain1, Lee R Krumholz1 and Mostafa S Elshahed2

  1. 1Department of Botany and Microbiology and Institute for Energy and the Environment, University of Oklahoma, Norman, OK, USA
  2. 2Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA

Correspondence: MS Elshahed, Department of Microbiology and Molecular Genetics, Oklahoma State University, 1110 S. Innovation way, Stillwater, OK 74074, USA. E-mail: mostafa@okstate.edu

Received 5 February 2009; Revised 23 March 2009; Accepted 27 March 2009; Published online 30 April 2009.

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Abstract

Small subunit (16S) rRNA gene surveys generating near full-length 16S rRNA clones offer a unique opportunity for in-depth phylogenetic analysis to highlight the breadth of diversity within various major bacterial phyla encountered in soil. This study offers a detailed phylogenetic analysis of the Proteobacteria-affiliated clones identified from 13001 nearly full-length 16S rRNA gene clones derived from Oklahoma tall-grass prairie soil. Proteobacteria was the most abundant phylum in the community, and comprised 25% of the total clones. The most abundant and diverse class within the Proteobacteria was Alphaproteobacteria, followed by the Delta-, Beta- and Gammaproteobacteria. Members of the Epsilon- and Zetaproteobacteria were not detected in the dataset. Our analysis identified 15 novel order-level and 48 novel family-level Proteobacteria lineages. In addition, we show that the majority of Proteobacteria clones in the dataset belong to orders and families containing no described cultivated representatives (50% and 65%, respectively). An examination of the ecological distribution of the six most abundant Proteobacteria lineages in this dataset with no characterized pure culture representatives provided important information regarding their global distribution and environmental preferences. This level of novel phylogenetic diversity indicates that our understanding of the functions of soil microorganisms, even those belonging to phyla with numerous and diverse well-characterized cultured representatives such as the Proteobacteria, remains far from adequate.

Keywords:

microbial communities, culture-independent studies, Proteobacteria, soil