Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils

The extent of microbial community diversity in two similar sandy surface soils from Virginia and Delaware (USA) was analysed with a culture-independent small subunit ribosomal RNA (SSU rRNA) gene-based cloning approach with about 400–700 SSU rDNA clones obtained from each sample. While there were no operational taxonomic units (OTUs) having more than three individuals, about 96–99% of the OTUs had only a single individual. The clones showing less than 85% similarity to the sequences in the current databases were fully sequenced. The majority of the clones (55%) had sequences that were more than 20% different from those in the current databases. About 37% of the clones differed by 15–20% in sequence from the database, 16% of the clones differed by 10–15%, and 5% of the clones differed by only 1–10%. Phylogenetic analysis indicated that these sequences fell into 10 of the 35–40 known phylogenetic divisions. Many of the clones were affiliated with Acidobacterium (35%). While a substantial portion of the clones belong to alpha (24%) and beta (12%) Proteobacteria, a few of them were affiliated with delta (6%) and gamma (3%) Proteobacteria. About 6% of the clones belong to Planctomycetes, and 4% of the clones were related to gram-positive bacteria. About 4% of clones were related to other bacterial divisions, including Cytophaga, Green sulfur bacteria, Nitrospira, OP10, and Verrucomicrobia. Eight sequences had no specific association with any of the known divisions or candidate divisions and were phylogenetically divided into three novel division level groups, named AD1, AD2 and AD3. Candidate division AD1 represented by six clones (4%) was found in both sites and consisted of two subdivisions. The community structures were similar between these two widely separated, sandy, oligotrophic, surface soils under grass vegetation in a temperate, humid climate but somewhat dissimilar to community structures revealed in similar studies in other types of soil habitats. Published by Elsevier Science Ltd.