Wide Distribution and Diversity of Members of the Bacterial Kingdom
            <i>Acidobacterium</i>
            in the Environment

Barns, Susan M.; Takala, Shannon L.; Kuske, Cheryl R.

doi:10.1128/aem.65.4.1731-1737.1999

Cited by 417 publications

(183 citation statements)

References 36 publications

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“…An important ¢nding was the cloning of a sequence from a mixed colony, which belongs to a group of environmental sequences with no cultured representative and only distant cultured relatives. These sequences have been found in direct analyses of several environmental samples, ranging from soil to sewage sludge and Antarctic ice ( [9,11,37,38] and GenBank accession numbers af173822 and af173824) and probably fall within the novel phylogenetic branch containing Acidobacterium capsulatum and Holophaga foetida. Several other similarly deep-branching clusters of cloned sequences from these samples have been found associated with this lineage [11].…”

Section: Discussionmentioning

confidence: 96%

Impact of cultivation on characterisation of species composition of soil bacterial communities

McCaig

2001

FEMS Microbiology Ecology

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The species composition of culturable bacteria in Scottish grassland soils was investigated using a combination of Biolog and 16S rDNA analysis for characterisation of isolates. The inclusion of a molecular approach allowed direct comparison of sequences from culturable bacteria with sequences obtained during analysis of DNA extracted directly from the same soil samples. Bacterial strains were isolated on Pseudomonas isolation agar (PIA), a selective medium, and on tryptone soya agar (TSA), a general laboratory medium. In total, 12 and 21 morphologically different bacterial cultures were isolated on PIA and TSA, respectively. Biolog and sequencing placed PIA isolates in the same taxonomic groups, the majority of cultures belonging to the Pseudomonas (sensu stricto) group. However, analysis of 16S rDNA sequences proved more efficient than Biolog for characterising TSA isolates due to limitations of the Microlog database for identifying environmental bacteria. In general, 16S rDNA sequences from TSA isolates showed high similarities to cultured species represented in sequence databases, although TSA-8 showed only 92.5% similarity to the nearest relative, Bacillus insolitus. In general, there was very little overlap between the culturable and uncultured bacterial communities, although two sequences, PIA-2 and TSA-13, showed s 99% similarity to soil clones. A cloning step was included prior to sequence analysis of two isolates, TSA-5 and TSA-14, and analysis of several clones confirmed that these cultures comprised at least four and three sequence types, respectively. All isolate clones were most closely related to uncultured bacteria, with clone TSA-5.1 showing 99.8% similarity to a sequence amplified directly from the same soil sample. Interestingly, one clone, TSA-5.4, clustered within a novel group comprising only uncultured sequences. This group, which is associated with the novel, deep-branching Acidobacterium capsulatum lineage, also included clones isolated during direct analysis of the same soil and from a wide range of other sample types studied elsewhere. The study demonstrates the value of fine-scale molecular analysis for identification of laboratory isolates and indicates the culturability of approximately 1% of the total population but under a restricted range of media and cultivation conditions. ß

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Section: Discussionmentioning

confidence: 96%

Impact of cultivation on characterisation of species composition of soil bacterial communities

McCaig

2001

FEMS Microbiology Ecology

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“…Additionally, there is growing recognition of the importance of Acidobacteria in the soil environment Jones et al, 2009). Previously a broad lineage of taxa only discovered in soils through the use of molecular techniques, they have now been shown to be culturable using low pH media, low nutrients and long incubation times (Kishimoto et al, 1991;Barns et al, 1999;Sait et al, 2002;2006).…”

Section: Discussionmentioning

confidence: 99%

The bacterial biogeography of British soils

Griffiths

Thomson

James

et al. 2011

Environmental Microbiology

790

529

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Despite recognition of the importance of soil bacteria to terrestrial ecosystem functioning there is little consensus on the factors regulating belowground biodiversity. Here we present a multi-scale spatial assessment of soil bacterial community profiles across Great Britain (> 1000 soil cores), and show the first landscape scale map of bacterial distributions across a nation. Bacterial diversity and community dissimilarities, assessed using terminal restriction fragment length polymorphism, were most strongly related to soil pH providing a large-scale confirmation of the role of pH in structuring bacterial taxa. However, while α diversity was positively related to pH, the converse was true for β diversity (between sample variance in α diversity). β diversity was found to be greatest in acidic soils, corresponding with greater environmental heterogeneity. Analyses of clone libraries revealed the pH effects were predominantly manifest at the level of broad bacterial taxonomic groups, with acidic soils being dominated by few taxa (notably the group 1 Acidobacteria and Alphaproteobacteria). We also noted significant correlations between bacterial communities and most other measured environmental variables (soil chemistry, aboveground features and climatic variables), together with significant spatial correlations at close distances. In particular, bacterial and plant communities were closely related signifying no strong evidence that soil bacteria are driven by different ecological processes to those governing higher organisms. We conclude that broad scale surveys are useful in identifying distinct soil biomes comprising reproducible communities of dominant taxa. Together these results provide a baseline ecological framework with which to pursue future research on both soil microbial function, and more explicit biome based assessments of the local ecological drivers of bacterial biodiversity.

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“…Full-length sequence analysis is needed to further explore the a⁄liation of C47.23PG and N42.38PG with Acidobacterium. Although Acidobacterium has few cultivated members, DNA sequences from uncultivated representatives have been frequently recovered from soil [34,35] including forest environments [14,36].…”

Section: Acidobacteriummentioning

confidence: 99%

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

Chow

2002

FEMS Microbiology Ecology

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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.

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Wide Distribution and Diversity of Members of the Bacterial Kingdom Acidobacterium in the Environment

Cited by 417 publications

References 36 publications

Impact of cultivation on characterisation of species composition of soil bacterial communities

Impact of cultivation on characterisation of species composition of soil bacterial communities

The bacterial biogeography of British soils

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

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