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1.  Detection and differentiation of bacterial spores in a mineral matrix by Fourier transform infrared spectroscopy (FTIR) and chemometrical data treatment 
BMC Biophysics  2011;4:14.
Fourier transform infrared spectroscopy (FTIR) has been used as analytical tool in chemistry for many years. In addition, FTIR can also be applied as a rapid and non-invasive method to detect and identify microorganisms. The specific and fingerprint-like spectra allow - under optimal conditions - discrimination down to the species level. The aim of this study was to develop a fast and reproducible non-molecular method to differentiate pure samples of Bacillus spores originating from different species as well as to identify spores in a simple matrix, such as the clay mineral, bentonite.
We investigated spores from pure cultures of seven different Bacillus species by FTIR in reflection or transmission mode followed by chemometrical data treatment. All species investigated (B. atrophaeus, B. brevis, B. circulans, B. lentus, B. megaterium, B. subtilis, B. thuringiensis) are typical aerobic soil-borne spore formers. Additionally, a solid matrix (bentonite) and mixtures of benonite with spores of B. megaterium at various wt/wt ratios were included in the study. Both hierarchical cluster analysis and principal component analysis of the spectra along with multidimensional scaling allowed the discrimination of different species and spore-matrix-mixtures.
Our results show that FTIR spectroscopy is a fast method for species-level discrimination of Bacillus spores. Spores were still detectable in the presence of the clay mineral bentonite. Even a tenfold excess of bentonite (corresponding to 2.1 × 1010 colony forming units per gram of mineral matrix) still resulted in an unambiguous identification of B. megaterium spores.
PMCID: PMC3155104  PMID: 21756333
Bacillus spores; infrared spectroscopy; FTIR; clay minerals; bentonite; mineral matrix
2.  Detection of Bacterial Endospores in Soil by Terbium Fluorescence 
Spore formation is a survival mechanism of microorganisms when facing unfavorable environmental conditions resulting in “dormant” states. We investigated the occurrence of bacterial endospores in soils from various locations including grasslands (pasture, meadow), allotment gardens, and forests, as well as fluvial sediments. Bacterial spores are characterized by their high content of dipicolinic acid (DPA). In the presence of terbium, DPA forms a complex showing a distinctive photoluminescence spectrum. DPA was released from soil by microwaving or autoclaving. The addition of aluminium chloride reduced signal quenching by interfering compounds such as phosphate. The highest spore content (up to 109 spores per gram of dry soil) was found in grassland soils. Spore content is related to soil type, to soil depth, and to soil carbon-to-nitrogen ratio. Our study might provide a basis for the detection of “hot spots” of bacterial spores in soil.
PMCID: PMC3132637  PMID: 21754939
3.  Weathering-Associated Bacteria from the Damma Glacier Forefield: Physiological Capabilities and Impact on Granite Dissolution ▿  
Applied and Environmental Microbiology  2010;76(14):4788-4796.
Several bacterial strains isolated from granitic rock material in front of the Damma glacier (Central Swiss Alps) were shown (i) to grow in the presence of granite powder and a glucose-NH4Cl minimal medium without additional macro- or micronutrients and (ii) to produce weathering-associated agents. In particular, four bacterial isolates (one isolate each of Arthrobacter sp., Janthinobacterium sp., Leifsonia sp., and Polaromonas sp.) were weathering associated. In comparison to what was observed in abiotic experiments, the presence of these strains caused a significant increase of granite dissolution (as measured by the release of Fe, Ca, K, Mg, and Mn). These most promising weathering-associated bacterial species exhibited four main features rendering them more efficient in mineral dissolution than the other investigated isolates: (i) a major part of their bacterial cells was attached to the granite surfaces and not suspended in solution, (ii) they secreted the largest amounts of oxalic acid, (iii) they lowered the pH of the solution, and (iv) they formed significant amounts of HCN. As far as we know, this is the first report showing that the combined action of oxalic acid and HCN appears to be associated with enhanced elemental release from granite, in particular of Fe. This suggests that extensive microbial colonization of the granite surfaces could play a crucial role in the initial soil formation in previously glaciated mountain areas.
PMCID: PMC2901745  PMID: 20525872
4.  Host-Plant Selectivity of Rhizobacteria in a Crop/Weed Model System 
PLoS ONE  2007;2(9):e846.
Belowground microorganisms are known to influence plants' performance by altering the soil environment. Plant pathogens such as cyanide-producing strains of the rhizobacterium Pseudomonas may show strong host-plant selectivity. We analyzed interactions between different host plants and Pseudomonas strains and tested if these can be linked to the cyanide sensitivity of host plants, the cyanide production of bacterial strains or the plant identity from which strains had been isolated. Eight strains (four cyanide producing) were isolated from roots of four weed species and then re-inoculated on the four weed and two additional crop species. Bacterial strain composition varied strongly among the four weed species. Although all six plant species showed different reductions in root growth when cyanide was artificially applied to seedlings, they were generally not negatively affected by inoculation with cyanide-producing bacterial strains. We found a highly significant plant species x bacterial strain interaction. Partitioning this interaction into contrasts showed that it was entirely due to a strongly negative effect of a bacterial strain (Pseudomonas kilonensis/brassicacearum, isolated from Galium mollugo) on Echinochloa crus-galli. This exotic weed may not have become adapted to the bacterial strain isolated from a native weed. Our findings suggest that host-specific rhizobacteria hold some promise as biological weed-control agents.
PMCID: PMC1952140  PMID: 17786217
5.  Influence of plant diversity and elevated atmospheric carbon dioxide levels on belowground bacterial diversity 
BMC Microbiology  2006;6:68.
Changes in aboveground plant species diversity as well as variations of environmental conditions such as exposure of ecosystems to elevated concentrations of atmospheric carbon dioxide may lead to changes in metabolic activity, composition and diversity of belowground microbial communities, both bacterial and fungal.
We examined soil samples taken from a biodiversity × CO2 grassland experiment where replicate plots harboring 5, 12, or 31 different plant species had been exposed to ambient or elevated (600 ppm) levels of carbon dioxide for 5 years. Analysis of soil bacterial communities in these plots by temporal temperature gradient gel electrophoresis (TTGE) showed that dominant soil bacterial populations varied only very little between different experimental treatments. These populations seem to be ubiquitous. Likewise, screening of samples on a high-resolution level by terminal restriction fragment length polymorphism (T-RFLP) showed that increased levels of carbon dioxide had no significant influence on both soil bacterial community composition (appearance and frequency of operational taxonomic units, OTUs) and on bacterial richness (total number of different OTUs). In contrast, differences in plant diversity levels had a significant effect on bacterial composition but no influence on bacterial richness. Regarding species level, several bacterial species were found only in specific plots and were related to elevated carbon dioxide or varying plant diversity levels. For example, analysis of T-RFLP showed that the occurrence of Salmonella typhimurium was significantly increased in plots exposed to elevated CO2 (P < 0.05).
Plant diversity levels are affecting bacterial composition (bacterial types and their frequency of occurrence). Elevated carbon dioxide does not lead to quantitative alteration (bacterial richness), whereas plant diversity is responsible for qualitative changes (bacterial diversity).
PMCID: PMC1552073  PMID: 16872510
6.  Effects of natural and chemically synthesized furanones on quorum sensing in Chromobacterium violaceum 
BMC Microbiology  2004;4:25.
Cell to cell signaling systems in Gram-negative bacteria rely on small diffusible molecules such as the N-acylhomoserine lactones (AHL). These compounds are involved in the production of antibiotics, exoenzymes, virulence factors and biofilm formation. They belong to the class of furanone derivatives which are frequently found in nature as pheromones, flavor compounds or secondary metabolites. To obtain more information on the relation between molecular structure and quorum sensing, we tested a variety of natural and chemically synthesized furanones for their ability to interfere with the quorum sensing mechanism using a quantitative bioassay with Chromobacterium violaceum CV026 for antagonistic and agonistic action. We were looking at the following questions:
1. Do these compounds affect growth?
2) Do these compounds activate the quorum sensing system of C. violaceum CV026?
3) Do these compounds inhibit violacein formation induced by the addition of the natural inducer N-hexanoylhomoserine lactone (HHL)?
4) Do these compounds enhance violacein formation in presence of HHL?
The naturally produced N-acylhomoserine lactones showed a strong non-linear concentration dependent influence on violacein production in C. violaceum with a maximum at 3.7*10-8 M with HHL. Apart from the N-acylhomoserine lactones only one furanone (emoxyfurane) was found to simulate N-acylhomoserine lactone activity and induce violacein formation. The most effective substances acting negatively both on growth and quorum sensing were analogs and intermediates in synthesis of the butenolides from Streptomyces antibioticus.
As the regulation of many bacterial processes is governed by quorum sensing systems, the finding of natural and synthetic furanones acting as agonists or antagonists suggests an interesting tool to control and handle detrimental AHL induced effects.
Some effects are due to general toxicity; others are explained by a competitive interaction for LuxR proteins. For further experiments it is important to be aware of the fact that quorum sensing active compounds have non-linear effects. Inducers can act as inhibitors and inhibitors might be able to activate or enhance the quorum sensing system depending on chemical structure and concentration levels.
PMCID: PMC509243  PMID: 15233843
7.  Development of a Laboratory-Scale Leaching Plant for Metal Extraction from Fly Ash by Thiobacillus Strains 
Semicontinuous biohydrometallurgical processing of fly ash from municipal waste incineration was performed in a laboratory-scale leaching plant (LSLP) by using a mixed culture of Thiobacillus thiooxidans and Thiobacillus ferrooxidans. The LSLP consisted of three serially connected reaction vessels, reservoirs for a fly ash suspension and a bacterial stock culture, and a vacuum filter unit. The LSLP was operated with an ash concentration of 50 g liter−1, and the mean residence time was 6 days (2 days in each reaction vessel). The leaching efficiencies (expressed as percentages of the amounts applied) obtained for the economically most interesting metal, Zn, were up to 81%, and the leaching efficiencies for Al were up to 52%. Highly toxic Cd was completely solubilized (100%), and the leaching efficiencies for Cu, Ni, and Cr were 89, 64, and 12%, respectively. The role of T. ferrooxidans in metal mobilization was examined in a series of shake flask experiments. The release of copper present in the fly ash as chalcocite (Cu2S) or cuprite (Cu2O) was dependent on the metabolic activity of T. ferrooxidans, whereas other metals, such as Al, Cd, Cr, Ni, and Zn, were solubilized by biotically formed sulfuric acid. Chemical leaching with 5 N H2SO4 resulted in significantly increased solubilization only for Zn. The LSLP developed in this study is a promising first step toward a pilot plant with a high capacity to detoxify fly ash for reuse for construction purposes and economical recovery of valuable metals.
PMCID: PMC106135  PMID: 16349536
8.  Pseudomonas oleovorans as a Source of Poly(β-Hydroxyalkanoates) for Potential Applications as Biodegradable Polyesters 
Pseudomonas oleovorans was grown in homogeneous media containing n-alkanoic acids, from formate to decanoate, as the sole carbon sources. Formation of intracellular poly(β-hydroxyalkanoates) was observed only for hexanoate and the higher n-alkanoic acids. The maximum isolated polymer yields were approximately 30% of the cellular dry weight with growth on either octanoate or nonanoate. In most cases, the major repeating unit in the polymer had the same chain length as the n-alkanoic acid used for growth, but units with two carbon atoms less or more than the acid used as a carbon source were also generally present in the polyesters formed. Indeed, copolymers containing as many as six different types of β-hydroxyalkanoate units were formed. The weight average molecular weights of the poly(β-hydroxyalkanoate) copolymers produced by P. oleovorans ranged from 90,000 to 370,000. In spite of the higher cell yields obtained with octanoate and nonanoate, the use of hexanoate and heptanoate yielded higher-molecular-weight polymers. These copolyesters represent an entirely new class of biodegradable thermoplastics.
PMCID: PMC202789  PMID: 16347708

Results 1-8 (8)