Alexandra Weilharter

Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment.

ABSTRACT Soil structure depends on the association between mineral soil particles (sand, silt, and clay) and organic matter, in which aggregates of different size and stability are formed. Although the chemistry of organic materials, total microbial biomass, and different enzyme activities in different soil particle size fractions have been well studied, little information is available on the structure of microbial populations in microhabitats. In this study, topsoil samples of different fertilizer treatments of a long-term field experiment were analyzed. Size fractions of 200 to 63 μm (fine sand fraction), 63 to 2 μm (silt fraction), and 2 to 0.1 μm (clay fraction) were obtained by a combination of low-energy sonication, wet sieving, and repeated centrifugation. Terminal restriction fragment length polymorphism analysis and cloning and sequencing of 16S rRNA genes were used to compare bacterial community structures in different particle size fractions. The microbial community structure was significantly affected by particle size, yielding higher diversity of microbes in small size fractions than in coarse size fractions. The higher biomass previously found in silt and clay fractions could be attributed to higher diversity rather than to better colonization of particular species. Low nutrient availability, protozoan grazing, and competition with fungal organisms may have been responsible for reduced diversities in larger size fractions. Furthermore, larger particle sizes were dominated by α-Proteobacteria, whereas high abundance and diversity of bacteria belonging to the Holophaga/Acidobacteriumdivision were found in smaller size fractions. Although very contrasting organic amendments (green manure, animal manure, sewage sludge, and peat) were examined, our results demonstrated that the bacterial community structure was affected to a greater extent by the particle size fraction than by the kind of fertilizer applied. Therefore, our results demonstrate specific microbe-particle associations that are affected to only a small extent by external factors.

Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis.

Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N(2)-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.

mRNA-Based Parallel Detection of Active Methanotroph Populations by Use of a Diagnostic Microarray

ABSTRACT A method was developed for the mRNA-based application of microbial diagnostic microarrays to detect active microbial populations. DNA- and mRNA-based analyses of environmental samples were compared and confirmed via quantitative PCR. Results indicated that mRNA-based microarray analyses may provide additional information on the composition and functioning of microbial communities.

RNA isolation from soil for bacterial community and functional analysis: evaluation of different extraction and soil conservation protocols

The impact of three different RNA isolation methods on the community analysis of metabolically active bacteria was determined by reverse transcription (RT) and PCR amplification of 16S rRNA genes and subsequent terminal restriction fragment length polymorphism (T-RFLP) analysis. Furthermore, soil samples were stored at different conditions in order to evaluate the effect of soil conservation methods on the outcome of the population analysis. The quality of mRNA was assessed by reverse transcription and PCR amplification of eubacterial glutamine synthetase genes. Our results indicated that the community composition as well as the abundance of individual members were affected by the kind of RNA isolation method. Furthermore, the extraction method influenced the recovery of mRNA. Lyophilization, storage at -20 degrees C as well as storage in glycerol stocks at -80 degrees C proved to be equally appropriate for the storage of soils and subsequent RNA isolation.

COMPLETE GENOME SEQUENCE OF THE PLANT GROWTH-PROMOTING ENDOPHYTE BURKHOLDERIA PHYTOFIRMANS STRAIN PsJN

Burkholderia phytofirmans PsJN(T) is able to efficiently colonize the rhizosphere, root, and above-ground plant tissues of a wide variety of genetically unrelated plants, such as potatoes, canola, maize, and grapevines. Strain PsJN shows strong plant growth-promoting effects and was reported to enhance plant vigor and resistance to biotic and abiotic stresses. Here, we report the genome sequence of this strain, which indicates the presence of multiple traits relevant for endophytic colonization and plant growth promotion.