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Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils

Authors

  • Bärbel U. Foesel,

    1. Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Planegg- Martinsried, Germany
    2. Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
    Current affiliation:
    1. Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
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  • Verena Nägele,

    1. Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Planegg- Martinsried, Germany
    Current affiliation:
    1. Pullacher Platz 7, 81371 München, Germany
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  • Astrid Naether,

    1. Abt. Mikrobielle Ökophysiologie, Fachbereich Biologie/Chemie, Universität Bremen, Bremen, Germany
    Current affiliation:
    1. Max Planck Institut für terrestrische Mikrobiologie, Marburg, Germany
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  • Pia K. Wüst,

    1. Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
    Current affiliation:
    1. Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
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  • Jan Weinert,

    1. Biologisches Institut, Universität Köln, Köln, Germany
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  • Michael Bonkowski,

    1. Biologisches Institut, Universität Köln, Köln, Germany
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  • Gertrud Lohaus,

    1. Abt. Forstbotanik und Baumphysiologie, Universität Göttingen, Göttingen, Germany
    Current affiliation:
    1. Molekulare Pflanzenforschung, Bergische Universität Wuppertal, Wuppertal, Germany
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  • Andrea Polle,

    1. Abt. Forstbotanik und Baumphysiologie, Universität Göttingen, Göttingen, Germany
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  • Fabian Alt,

    1. Universität Koblenz, Koblenz, Germany
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  • Yvonne Oelmann,

    1. Universität Koblenz, Koblenz, Germany
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  • Markus Fischer,

    1. Institut für Pflanzenökologie, Universität Bern, Bern, Switzerland
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  • Michael W. Friedrich,

    1. Abt. Mikrobielle Ökophysiologie, Fachbereich Biologie/Chemie, Universität Bremen, Bremen, Germany
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  • Jörg Overmann

    Corresponding author
    1. Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Planegg- Martinsried, Germany
    2. Technische Universität Braunschweig, Braunschweig, Germany
    3. Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
    Current affiliation:
    1. Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
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Summary

16S rRNA genes and transcripts of Acidobacteria were investigated in 57 grassland and forest soils of three different geographic regions. Acidobacteria contributed 9–31% of bacterial 16S rRNA genes whereas the relative abundances of the respective transcripts were 4–16%. The specific cellular 16S rRNA content (determined as molar ratio of rRNA : rRNA genes) ranged between 3 and 80, indicating a low in situ growth rate. Correlations with flagellate numbers, vascular plant diversity and soil respiration suggest that biotic interactions are important determinants of Acidobacteria 16S rRNA transcript abundances in soils. While the phylogenetic composition of Acidobacteria differed significantly between grassland and forest soils, high throughput denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism fingerprinting detected 16S rRNA transcripts of most phylotypes in situ. Partial least squares regression suggested that chemical soil conditions such as pH, total nitrogen, C : N ratio, ammonia concentrations and total phosphorus affect the composition of this active fraction of Acidobacteria. Transcript abundance for individual Acidobacteria phylotypes was found to correlate with particular physicochemical (pH, temperature, nitrogen or phosphorus) and, most notably, biological parameters (respiration rates, abundances of ciliates or amoebae, vascular plant diversity), providing culture-independent evidence for a distinct niche specialization of different Acidobacteria even from the same subdivision.

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