Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment

Abstract

To assess the distribution and diversity of members of the recently identified bacterial kingdom Acidobacterium, members of this kingdom present in 43 environmental samples were surveyed by PCR amplification. A primer designed to amplify rRNA gene sequences (ribosomal DNAs [rDNAs]) from most known members of the kingdom was used to interrogate bulk DNA extracted from the samples. Positive PCR results were obtained with all temperate soil and sediment samples tested, as well as some hot spring samples, indicating that members of this kingdom are very widespread in terrestrial environments. PCR primers specific for four phylogenetic subgroups within the kingdom were used in similar surveys. All four subgroups were detected in most neutral soils and some sediments, while only two of the groups were seen in most low-pH environments. The combined use of these primers allowed identification of a novel lineage within the kingdom in a hot spring environment. Phylogenetic analysis of rDNA sequences from our survey and the literature outlines at least six major subgroups within the kingdom. Taken together, these data suggest that members of the Acidobacterium kingdom are as genetically and metabolically diverse, environmentally widespread and perhaps as ecologically important as the well-known Proteobacteria and gram-positive bacterial kingdoms.

FIG. 1

Phylogenetic tree representing the known diversity of the kingdom Acidobacterium. Sequences (other than GFP1) were obtained from databases and unpublished sources and analyzed as described in the text. The source references for the sequences shown are as follows: Amaz. (Amazon) forest/Amaz. pasture, ; Aust. (Australian) forest, and ; freshwater sediment, ; forest soil, ; grassland peat (TM sequences), ; grassland peat (DA sequences), ; acid mine drainage, ; lake sediment, ; clover pasture, ; Siberian tundra, ; pinyon-juniper forest/pinyon rhizosphere/volcanic cinders, ; hot spring sediment (OP), ; agricultural soil, ; rice paddy, ; and contaminated aquifer, . Others are unpublished sequences from GenBank. Bootstrap values for MP analysis are given for branches having >60% support. Phylogenetic groups are designated based on primary branching clades appearing in all (ML, MP, and DM) optimal trees and having >85% bootstrap support, based on long (>900 nt) sequences (heavy lines). Partial sequences (thin lines) represent sequences added to the optimized ML tree without global rearrangement. The tree was rooted with the rRNA sequence of E. coli. The primer groups are those sequences expected to amplify with the primers listed in Tables 1 and 2.