Identifying the Dominant Soil Bacterial taxa in Libraries. of 16S rRNA and 16S rRNA Genes

Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia.
Applied and Environmental Microbiology (Impact Factor: 3.67). 04/2006; 72(3):1719-28. DOI: 10.1128/AEM.72.3.1719-1728.2006
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Available from: Peter H Janssen, Sep 15, 2014
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    • "Brevundimonas sp. belongs to the class Proteobacteria, which has been shown to contain Asresistant bacteria (Janssen, 2006). Among three PV tissues, Bacillus sp. was present only in the roots. "
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    ABSTRACT: The ability of As-resistant endophytic bacteria in As transformation and plant growth promotion was determined. The endophytes were isolated from As-hyperaccumulator Pteris vittata (PV) after growing for 60 d in a soil containing 200 mg kg(-1) arsenate (AsV). They were isolated in presence of 10 mM AsV from PV roots, stems, and leaflets, representing 4 phyla and 17 genera. All endophytes showed at least one plant growth promoting characteristics including IAA synthesis, siderophore production and P solubilization. The root endophytes had higher P solubilization ability than the leaflet (60.0 vs. 18.3 mg L(-1)). In presence of 10 mM AsV, 6 endophytes had greater growth than the control, suggesting As-stimulated growth. Furthermore, root endophytes were more resistant to AsV while the leaflet endophytes were more tolerant to arsenite (AsIII), which corresponded to the dominant As species in PV tissues. Bacterial As resistance was positively correlated to their ability in AsV reduction but not AsIII oxidation. The roles of those endophytes in promoting plant growth and As resistance in P. vittata warrant further investigation.
    Chemosphere 02/2016; 144C:1233-1240. DOI:10.1016/j.chemosphere.2015.09.102 · 3.34 Impact Factor
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    • ", 2009 ; Chong et al . , 2012b ) , including common groups found in soil ecosystems globally such as Acidobacteria , Proteobacteria , Firmicutes , and Bacteroidetes ( Janssen , 2006 ; Youssef and Elshahed , 2008 ) . Nevertheless , in comparisons across different Antarctic regions , strong compositional differences become apparent . "
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    ABSTRACT: Recent advances in knowledge of patterns of biogeography in terrestrial eukaryotic organisms have led to a fundamental paradigm shift in understanding of the controls and history of life on land in Antarctica, and its interactions over the long term with the glaciological and geological processes that have shaped the continent. However, while it has long been recognized that the terrestrial ecosystems of Antarctica are dominated by microbes and their processes, knowledge of microbial diversity and distributions has lagged far behind that of the macroscopic eukaryote organisms. Increasing human contact with and activity in the continent is leading to risks of biological contamination and change in a region whose isolation has protected it for millions of years at least; these risks may be particularly acute for microbial communities which have, as yet, received scant recognition and attention. Even a matter apparently as straightforward as Protected Area designation in Antarctica requires robust biodiversity data which, in most parts of the continent, remain almost completely unavailable. A range of important contributing factors mean that it is now timely to reconsider the state of knowledge of Antarctic terrestrial prokaryotes. Rapid advances in molecular biological approaches are increasingly demonstrating that bacterial diversity in Antarctica may be far greater than previously thought, and that there is overlap in the environmental controls affecting both Antarctic prokaryotic and eukaryotic communities. Bacterial dispersal mechanisms and colonization patterns remain largely unaddressed, although evidence for regional evolutionary differentiation is rapidly accruing and, with this, there is increasing appreciation of patterns in regional bacterial biogeography in this large part of the globe. In this review, we set out to describe the state of knowledge of Antarctic prokaryote diversity patterns, drawing analogy with those of eukaryote groups where appropriate. Based on our synthesis, it is clear that spatial patterns of Antarctic prokaryotes can be unique at local scales, while the limited evidence available to date supports the group exhibiting overall regional biogeographical patterns similar to the eukaryotes. We further consider the applicability of the concept of “functional redundancy” for the Antarctic microbial community and highlight the requirements for proper consideration of their important and distinctive roles in Antarctic terrestrial ecosystems.
    Frontiers in Microbiology 09/2015; 6. DOI:10.3389/fmicb.2015.01058 · 3.99 Impact Factor
    • "Abundance of the total group and of phylum-specific groups The abundance levels of total bacteria, phylum-specific groups, and Crenarchaea were quantified by quantitative PCR (qPCR) targeting 16S rRNA sequences, as previously described (Petrić et al. 2011). Taxon-specific primer pairs were used to quantify Actinobacteria, Acidobacteria, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Archaea—Crenarchaeota (Muyzer et al. 1993; Ochsenreiter et al. 2003; Fierer et al. 2005; Mühling et al. 2008; Philippot et al. 2009) known to represent up to 90 % of the soil bacterial community (Janssen 2006). Each qPCR assay was conducted in a ViiA7™ thermocycler (Life Technologies) in a 15-μL final reaction volume containing 1× SYBR green PCR "
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    ABSTRACT: The insecticide chlordecone applied for decades in banana plantations currently contaminates 20,000 ha of arable land in the French West Indies. Although the impact of various pesticides on soil microorganisms has been studied, chlordecone toxicity to the soil microbial community has never been assessed. We investigated in two different soils (sandy loam and silty loam) exposed to different concentrations of CLD (D0, control; D1 and D10, 1 and 10 times the agronomical dose) over different periods of time (3, 7, and 32 days): (i) the fate of chlordecone by measuring (14)C-chlordecone mass balance and (ii) the impact of chlordecone on microbial community structure, abundance, and function, using standardized methods (-A-RISA, taxon-specific quantitative PCR (qPCR), and (14)C-compounds mineralizing activity). Mineralization of (14)C-chlordecone was inferior below 1 % of initial (14)C-activity. Less than 2 % of (14)C-activity was retrieved from the water-soluble fraction, while most of it remained in the organic-solvent-extractable fraction (75 % of initial (14)C-activity). Only 23 % of the remaining (14)C-activity was measured in nonextractable fraction. The fate of chlordecone significantly differed between the two soils. The soluble and nonextractable fractions were significantly higher in sandy loam soil than in silty loam soil. All the measured microbiological parameters allowed discriminating statistically the two soils and showed a variation over time. The genetic structure of the bacterial community remained insensitive to chlordecone exposure in silty loam soil. In response to chlordecone exposure, the abundance of Gram-negative bacterial groups (β-, γ-Proteobacteria, Planctomycetes, and Bacteroidetes) was significantly modified only in sandy loam soil. The mineralization of (14)C-sodium acetate and (14)C-2,4-D was insensitive to chlordecone exposure in silty loam soil. However, mineralization of (14)C-sodium acetate was significantly reduced in soil microcosms of sandy loam soil exposed to chlordecone as compared to the control (D0). These data show that chlordecone exposure induced changes in microbial community taxonomic composition and function in one of the two soils, suggesting microbial toxicity of this organochlorine.
    Environmental Science and Pollution Research 05/2015; DOI:10.1007/s11356-015-4758-2 · 2.83 Impact Factor
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