Publications (4)8.2 Total impact
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Article: Improved protocol for the simultaneous extraction and column-based separation of DNA and RNA from different soils.
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ABSTRACT: We developed an improved protocol, allowing the simultaneous extraction of DNA and RNA from soil using phenol-chloroform with subsequent column-based separation of DNA and RNA (PCS). We compared this new approach with the well established protocol published by Griffiths et al. (2000), where DNA and RNA are separated by selective enzymatic digestions and two commercial kits used for DNA or RNA extraction, respectively, using four different agricultural soils. We compared yield and purity of the nucleic acids as well as abundance and diversity profiles of the soil bacterial communities targeting the nosZ gene via quantitative real-time PCR and terminal restriction fragment length polymorphism on DNA and RNA level. The newly developed protocol provided purer nucleic acid extracts compared to the used kit-based protocols. All protocols were suitable for DNA- and RNA-based gene quantification, however high variations between replicates were obtained for RNA samples using the original Griffiths protocol. Diversity patterns of nosZ were highly influenced by the extraction protocol used both on the DNA and RNA level. Finally, our data showed that the new protocol allows a simultaneous and reproducible extraction and separation of DNA and RNA, which were suitable for reliable analyses of gene and transcript copy numbers and diversity pattern.Journal of microbiological methods 01/2011; 84(3):406-12. · 2.43 Impact Factor -
Article: Quantification of key genes steering the microbial nitrogen cycle in the rhizosphere of sorghum cultivars in tropical agroecosystems.
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ABSTRACT: The effect of agricultural management practices on geochemical cycles in moderate ecosystems is by far better understood than in semiarid regions, where fertilizer availability and climatic conditions are less favorable. We studied the impact of different fertilizer regimens in an agricultural long-term observatory in Burkina Faso at three different plant development stages (early leaf development, flowering, and senescence) of sorghum cultivars. Using real-time PCR, we investigated functional microbial communities involved in key processes of the nitrogen cycle (nitrogen fixation, ammonia oxidation, and denitrification) in the rhizosphere. The results indicate that fertilizer treatments and plant development stages combined with environmental factors affected the abundance of the targeted functional genes in the rhizosphere. While nitrogen-fixing populations dominated the investigated communities when organic fertilizers (manure and straw) were applied, their numbers were comparatively reduced in urea-treated plots. In contrast, ammonia-oxidizing bacteria (AOB) increased not only in absolute numbers but also in relation to the other bacterial groups investigated in the urea-amended plots. Ammonia-oxidizing archaea exhibited higher numbers compared to AOB independent of fertilizer application. Similarly, denitrifiers were also more abundant in the urea-treated plots. Our data imply as well that, more than in moderate regions, water availability might shape microbial communities in the rhizosphere, since low gene abundance data were obtained for all tested genes at the flowering stage, when water availability was very limited.Applied and environmental microbiology 07/2009; 75(15):4993-5000. · 3.69 Impact Factor -
Article: In vitro antagonism of an actinobacterial Kitasatospora isolate against the plant pathogen Phytophthora citricola as elucidated with ultrahigh resolution mass spectrometry.
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ABSTRACT: Many soil microorganisms antagonistic to soil borne plant pathogens are well known for their ability to control diseases in situ. A variety of substances, like lytic enzymes, siderophores and antibiotics, produced by these organisms have the potential to protect roots against pathogens. Understanding the ecology and a functional assessment of antagonistic microbial communities in soil requires in-depth knowledge of the mechanisms involved in these interactions, a challenging task in complex systems if low-resolution methods are applied. We propose an information-rich strategy of general relevance, composed of adequate preconcentration in conjunction with ultrahigh resolution ion cyclotron resonance Fourier transform mass spectrometry (ICR-FT/MS) and nuclear magnetic resonance (NMR) spectroscopy to identify any bioactive substances in complex systems. This approach is demonstrated on the specific example of substance identification considered responsible for in vitro antagonism of an actinobacterial antagonist isolated from European beech (Fagus sylvatica) rhizosphere soil against the oomycetous root rot pathogen Phytophthora citricola. The isolate belonging to the genus Kitasatospora exhibited strong antibiosis against the oomycete in vitro. The bioactive substance was observed to exhibit a molar mass of 281.1699 g/mol in positive electrospray ionization mass spectra, and the high mass accuracy of the ICR-FT/MS measurements allowed a precise assignment of a molecular formula that was found identical to the macrolide polyketide cycloheximide C(15)H(23)NO(4)+H(+); its identity was then unequivocally confirmed by the information-rich atomic signature of proton NMR spectroscopy. In conclusion, the combination of the near orthogonal methods (pre)fractionation, ultrahigh-resolution ICR-FT mass spectrometry (yielding molecular and MS(n) fragment signatures) and nuclear magnetic resonance spectroscopy (providing atomic signatures) has been found capable of identifying a biocontrol active compound of Kitasatospora active against Phytophthora citricola expediently, quickly, and accurately. This straightforward approach is of general applicability to elucidate biocontrol mechanisms in any complex system with improved efficiency.Journal of Microbiological Methods 07/2008; 75(2):188-95. · 2.09 Impact Factor -
Article: Microbial biocontrol of the pathogen Phytophthora citricola in the rhizosphere of European beech (Fagus sylvatica L.)
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ABSTRACT: Das Ziel dieser Untersuchungen war eine Analyse antagonistischer mikrobieller Interaktionen in der Rhizosphäre von Rotbuchen ( Fagus sylvatica ). Mikroorganismen wurden aus Rhizosphärenboden und von Feinwurzeln isoliert und auf Antagonismus gegenüber dem Wurzelpathogen Phytophthora citricola überprüft. Mittels Fourier Transform Ionenzyklotronresonanz Massenspektrometrie (FT-ICR/MS) in Kombination mit 1H-NMR konnte durch eine Metabolitenanalyse von Isolaten der Gattung Kitasatospora das Makrolid Polyketid Cycloheximid als biologisch aktive Substanz identifiziert werden. Basierend auf diesen Ergebnissen wurde ein Gewächshausexperiment durchgeführt, um den Einfluss biotischer (Inokulierung mit P. citricola ) und abiotischer (Erhöhung von CO<sub>2</sub> oder O<sub>3</sub>) Faktoren auf die strukturelle (Aktinobakterien 16S rRNA Gene) und funktionelle (Typ II Polyketide Synthasen) Diversität der antagonistischen, mikrobiellen Rhizosphärengemeinschaft zu untersuchen.
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Institutions
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2011
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University of Technology Munich
- Lehrstuhl für Bodenökologie
München, Bavaria, Germany
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2008–2009
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Helmholtz Zentrum München
- Institut für Bodenökologie
München, Bavaria, Germany
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