Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source

Abstract

Rhizosphere bacteria from Lodgepole pine (Pinus contorta) seedlings were characterized from forest soils which differed in disturbance and geographic source. Soil disturbance treatments included whole-tree harvesting with and without heavy soil compaction and whole-tree harvesting with complete surface organic matter removal and heavy soil compaction from British Columbia (BC) Ministry of Forests Long-Term Soil Productivity installations in three biogeoclimatic subzones in central BC, Canada. Bacterial community members were characterized by DNA sequence analysis of 16S rRNA gene fragments following direct DNA isolation from soil, polymerase chain reaction amplification and cloning. Phylogenetic analyses revealed that 85% of 709 16S rDNA clones were classified as K-, L-, Q-, and N-Proteobacteria, Actinobacteria, Cytophaga-Flexibacter-Bacteroides group, Acidobacterium, Verrucomicrobia, and candidate divisions OP10 and TM6. Members of the Proteobacteria and Acidobacterium represented 55% and 19% of the clone library, respectively, whereas the remaining bacterial divisions each comprised less than 4% of the clone library. One hundred and six 16S rDNA clones could not be classified into known bacterial divisions. No significant differences were detected for soil disturbance treatment or site effects on the proportions of 16S rDNA clones affiliated with Proteobacteria and Acidobacterium. Phylogenetic analyses revealed that it was common for 16S rRNA gene fragments from different soil disturbance treatments and geographic locations to be closely related.

Seasonal variation of microbial populations and biomass in Tatachia grassland soils of Taiwan

“…Acidobacteria and Proteobacteria are generally the most numerically dominant phyla in soil, while members of Bacteroidetes and Firmicutes are less common (Dunbar et al 1999;Chow et al 2002;Fierer et al 2005). In this study, we also found Proteobacteria and Acidobacteria to be dominant.…”

“…In this study, we also found Proteobacteria and Acidobacteria to be dominant. Members of aProteobacteria were the most abundant bacteria in 16S rDNA clone libraries derived from Long-Term Soil Productivity (LTSP) forest soil from British Columbia, Canada (Chow et al 2002), Australian forest soils (Stackebrandt et al 1993), Scotland grassland rhizosphere soil (McCaig et al 1999), and fertilizer-applied soil (Toyota and Kuninaga 2006). Members of Acidobacteria were the most abundant in the clone libraries from Arizona pinyon pine rhizosphere and bulk soils (Dunbar et al 1999), and in desert, prairie, and forest soils (Fierer et al 2005).…”

The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors

“…Culture-independent analyses performed with various plants often reveal that members of the (former) Cytophaga-Flavobacterium-Bacteroidetes constitute a dominant fraction of the rhizobacteria, as with Lolium perenne (Marilley and Aragno 1999), maize (Zea mays; Chelius and Triplett 2001) or Lodgepole pine (Pinus contorta; Chow et al 2002), and cucumber (Cucumis sativus; Green et al 2006). In this latter publication, in which the rhizobacteria associated with the transition from seeds to root were analyzed, Chryseobacterium (Bacteroidetes) and Oxalobacteraceae (ß proteobacteria) were the most persistent populations.…”

“…However, while Kaiser et al (2001) also found dominant Bacteroidetes populations in canola (Brassica napus), Smalla et al (2001) did not, although both studies appear to have been conducted at the same location. Other groups that may dominate the rhizosphere as shown by cultureindependent analyses, include Acidobacterium, Verrucomicrobia, Gemmatimonadetes and Nitrospirae (Ludwig et al 1997;Singh et al 2007;Filion et al 2004;Chow et al 2002).…”

“…Members of this group were found in the rhizosphere of two plant species endemic to South Africa, Leucospermum truncatulum and Leucandendron xanthoconus (Stafford et al 2005). Nineteen percent of a 16S rRNA gene-based clone library from Pinus contorta (Lodgepole pine) was found to originate from seven different subgroups of Acidobacteria (Chow et al 2002). In the rhizosphere of Thlaspi caerulescens, 14.5% of the 16S rRNA gene-based library clones were affiliated with acidobacterial sequences present in databases, belonging to five different subgroups (Gremion et al 2003).…”