Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil

• Published in: FEMS microbiology ecology Vol. 71; no. 1; pp. 23 - 33
• Main Authors: Kielak, Anna, Rodrigues, Jorge L.M, Kuramae, Eiko E, Chain, Patrick S.G, van Veen, Johannes A, Kowalchuk, George A
• Format: Journal Article
• Language: English
• Published: Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01-01-2010; Blackwell Publishing Ltd; Blackwell; Oxford University Press
• Subjects: Agricultural land; Agriculture; Agronomy. Soil science and plant productions; Animal, plant and microbial ecology; Annotations; Bacteria; Bacteria - classification; Bacteria - genetics; bacterial communities; Base Sequence; Biological and medical sciences; Cloning, Molecular; Cultivation; Deoxyribonucleic acid; DNA; DNA sequencing; DNA, Bacterial - chemistry; DNA, Bacterial - isolation & purification; Ecology; environmental genomics; Fundamental and applied biological sciences. Psychology; Gene order; Gene sequencing; Gene transfer; General agroecology; General agroecology. Agricultural and farming systems. Agricultural development. Rural area planning. Landscaping; General agronomy. Plant production; Generalities. Agricultural and farming systems. Agricultural development; Genome, Bacterial; Genomes; Genomics; Grasslands; Inserts; Metagenomics; Microbial ecology; Microbiology; Molecular Sequence Data; Operons; Phylogenetics; Phylogeny; Poaceae; rhizosphere; RNA, Ribosomal, 16S - genetics; rRNA 16S; Screening; Soil Microbiology; Soil microorganisms; Soils; Subdivisions; Various environments (extraatmospheric space, air, water); Verrucomicrobia; phylogeny; environmental genomics; bacterial communities; metagenomics; rhizosphere; Rhizosphere; Verrucomicrobia; Genomics; Environment; Agriculture; Phylogeny; Metagenome; Microbial community; Grassland soil
• ISSN: 0168-6496; 1574-6941
• DOI: 10.1111/j.1574-6941.2009.00785.x

The bacterial phylum Verrucomicrobia has a widespread distribution, and is known to be one of the most common and diverse phyla in soil habitats. However, members of this phylum have typically been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we examine the phylogenetic diversity of the Verrucomicrobia in a former agricultural field and gain access to genomic information via a metagenomic approach. We examined Verrucomicrobia-like 16S rRNA gene sequences recovered from general bacterial and phylum-specific libraries, revealing a dominance of subdivisions 1 and 2. A PCR-based screening method was developed to identify inserts containing verrucomicrobial 16S rRNA genes within a large-insert metagenomic library, and on screening of 28 800 clones, four fosmids were identified as containing verrucomicrobial genomic DNA. Full-length sequencing of fosmid inserts and gene annotation identified a total of 98 ORFs, representing a range of functions. No conservation of gene order was observed adjacent to the ribosomal operons. Fosmid inserts were further analyzed for tetranucleotide frequencies to identify remnants of past horizontal gene transfer events. The metagenomic approach utilized proved to be suitable for the recovery of verrucomicrobial genomic DNA, thereby providing a window into the genomes of members of this important, yet poorly characterized, bacterial phylum.