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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    • "Using this methodology, we were able to identify and discriminate between 12 different species of pigmented cocci soil bacteria belonging to three genera mainly Micrococcus, Deinococcus, and Kocuria that are highly abundant in soil (Ventura et al. 2007; Janssen 2006). Our results demonstrate the potential of Raman spectroscopy as a minimally invasive taxonomic tool to identify pigmented cocci soil bacteria. "
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    ABSTRACT: A soil habitat consists of a significant number of bacteria that cannot be cultivated by conventional means, thereby posing obvious difficulties in their classification and identification. This difficulty necessitates the need for advanced techniques wherein a well-compiled biomolecular database consisting of the already cultivable bacteria can be used as a reference in an attempt to link the noncultivable bacteria to their closest phylogenetic groups. Raman spectroscopy has been successfully applied to taxonomic studies of many systems like bacteria, fungi, and plants relying on spectral differences contributed by the variation in their overall biomolecular composition. However, these spectral differences can be obscured due to Raman signatures from photosensitive microbial pigments like carotenoids that show enormous variation in signal intensity hindering taxonomic investigations. In this study, we have applied laser-induced photobleaching to expel the carotenoid signatures from pigmented cocci bacteria. Using this method, we have investigated 12 species of pigmented bacteria abundant in soil habitats belonging to three genera mainly Micrococcus, Deinococcus, and Kocuria based on their Raman spectra with the assistance of a chemometric tool known as the radial kernel support vector machine (SVM). Our results demonstrate the potential of Raman spectroscopy as a minimally invasive taxonomic tool to identify pigmented cocci soil bacteria at a single-cell level.
    Environmental Science and Pollution Research 05/2015; DOI:10.1007/s11356-015-4593-5 · 2.83 Impact Factor
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    • "Actinobacteria can be found in terrestrial, freshwater and marine ecosystems, but more abundant in soil (Gremion et al., 2003; Janssen, 2006). The genus Streptomyces was first described by Waksman & Henrici (1943), widely distributed in nature. "
    04/2015; 30(1). DOI:10.17519/apiculture.2015.
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    • "Ca. 90% of all described prokaryotic species belong to only four of the 30 bacterial phyla (Yarza et al. 2014), whereas the majority of phyla are hardly represented by living isolates. For example, the phylum 'Acidobacteria' may comprise up to 50% of all soil bacteria (Janssen 2006) but currently only ca. 30 species are described. "
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    ABSTRACT: Prokaryotes ('Bacteria' and 'Archaea') are the most dominant and diverse form of life in soil and are indispensable for soil ecology and Earth system processes. This review addresses and interrelates the breadth of microbial biology in the global context of soil biology primarily for a readership less familiar with (soil) microbiology. First, the basic properties of prokaryotes and their major differences to macro-organisms are introduced. Further, technologies to study soil microbiology such as high-throughput next-generation sequencing and associated computational challenges are addressed. A brief insight into the principles of microbial systematics and taxonomy is provided. Second, the complexity and activity of microbial communities and the principles of their assembly are discussed, with a focus on the spatial distance of a few µm which is the scale at which prokaryotes perceive their environment. The interactions of prokaryotes with plant roots and soil fauna such as earthworms are addressed. Further, the role, resistance and resilience of prokaryotic soil communities in the light of anthropogenic disturbances such as global warming, elevated CO 2 and massive nitrogen and phosphorous fertilization is discussed. Finally, current discussions triggered by the above-addressed complexity of microbes in soil on whether microbial ecology needs a theory that is different from that of macroecology are viewed. Keywords spatial microbial ecology | nutrient cycling | high-throughput sequencing | OTU | ecological theory
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