Weitzel M.,Institute of Bio and Geosciences |
Weitzel M.,Jülich Research Center |
Noh K.,Institute of Bio and Geosciences |
Noh K.,Jülich Research Center |
And 8 more authors.
Bioinformatics | Year: 2013
13C-based metabolic flux analysis (13C-MFA) is the state-of-the-art method to quantitatively determine in vivo metabolic reaction rates in microorganisms. 13CFLUX2 contains all tools for composing flexible computational 13C-MFA workflows to design and evaluate carbon labeling experiments. A specially developed XML language, FluxML, highly efficient data structures and simulation algorithms achieve a maximum of performance and effectiveness. Support of multicore CPUs, as well as compute clusters, enables scalable investigations. 13CFLUX2 outperforms existing tools in terms of universality, flexibility and built-in features. Therewith, 13CFLUX2 paves the way for next-generation high-resolution 13C-MFA applications on the large scale. © The Author(s) 2012. Published by Oxford University Press.
Jablonowski N.D.,Institute of Bio and Geosciences |
Borchard N.,Jülich Research Center |
Zajkoska P.,Slovak University of Technology in Bratislava |
Fernandez-Bayo J.D.,IRD Montpellier |
And 3 more authors.
Journal of Agricultural and Food Chemistry | Year: 2013
Biochar addition to soil has been reported to reduce the microbial degradation of pesticides due to sorption of the active compound. This study investigated whether the addition of hardwood biochar alters the mineralization of 14C-labeled atrazine in two atrazine-adapted soils from Belgium and Brazil at different moisture regimens. Biochar addition resulted in an equally high or even in a significantly higher atrazine mineralization compared to the soils without biochar. Statistical analysis revealed that the extent of atrazine mineralization was more influenced by the specific soil than by the addition of biochar. It was concluded that biochar amendment up to 5% by weight does not negatively affect the mineralization of atrazine by an atrazine-adapted soil microflora. © 2012 American Chemical Society.
Jiang X.,Institute of Bio and Geosciences |
Bol R.,Institute of Bio and Geosciences |
Willbold S.,Jülich Research Center |
Vereecken H.,Institute of Bio and Geosciences |
Klumpp E.,Institute of Bio and Geosciences
Biogeosciences | Year: 2015
To maximize crop productivity fertilizer P is generally applied to arable soils, a significant proportion of which becomes stabilized by mineral components and in part subsequently becomes unavailable to plants. However, little is known about the relative contributions of the different organic and inorganic P bound to Fe/Al oxides in the smaller soil particles. Alkaline (NaOH-Na2EDTA) extraction with solution 31P-nuclear magnetic resonance (31P-NMR) spectroscopy is considered a reliable method for extracting and quantifying organic P and (some) inorganic P. However, any so-called residual P after the alkaline extraction has remained unidentified. Therefore, in the present study, the amorphous (a) and crystalline (c) Fe/Al oxide minerals and related P in soil aggregate-sized fractions (> 20, 2-20, 0.45-2 and < 0.45 μm) were specifically extracted by oxalate (a-Fe/Al oxides) and dithionite-citrate-bicarbonate (DCB, both a- and c-Fe/Al oxides). These soil aggregate-sized fractions with and without the oxalate and DCB pre-treatments were then sequentially extracted by alkaline extraction prior to solution 31P-NMR spectroscopy. This was done to quantify the P associated with a- and c-Fe/Al oxides in both alkaline extraction and the residual P of different soil aggregate-sized fractions. The results showed that overall P contents increased with decreasing size of the soil aggregate-sized fractions. However, the relative distribution and speciation of varying P forms were found to be independent of soil aggregate-size. The majority of alkaline-extractable P was in the a-Fe/Al oxide fraction (42-47 % of total P), most of which was ortho-phosphate (36-41 % of total P). Furthermore, still significant amounts of particularly monoester P were bound to these oxides. Intriguingly, however, Fe/Al oxides were not the main bonding sites for pyrophosphate. Residual P contained similar amounts of total P associated with both a-(11-15 % of total P) and c-Fe oxides (7-13 % of total P) in various aggregate-sized fractions, suggesting that it was likely occluded within the a- and c-Fe oxides in soil. This implies that, with the dissolution of Fe oxides, this P may be released and thus available for plants and microbial communities. © Author(s) 2015.
Farlin J.,CRP Henri Tudor |
Galle T.,CRP Henri Tudor |
Bayerle M.,CRP Henri Tudor |
Pittois D.,CRP Henri Tudor |
And 6 more authors.
Geoderma | Year: 2013
As a consequence of the repeated and widespread use of pesticides in agriculture, pesticide soil residues can be informative tracers of the spatial distribution of soil properties or of the application history. Atrazine, desethylatrazine and terbutylazine soil residues were measured in ninety-six soil samples taken on seventy-one contiguous fields four and a half years after the last atrazine application. The influence of soil texture and the application cycles were still clearly distinguishable in the spatial distribution of the pesticide residues. Half-lives calculated for a first order degradation kinetics from the atrazine and terbutylazine soil residues were within the range of values reported in the literature. The pesticide fate model PEARL calibrated on groundwater measurements underestimated slightly atrazine soil concentrations. The joint simulation of the fate of atrazine and its degradation product desethylatrazine also proved useful to estimate their respective half-lives and sorption parameters, and gave insight into degradation losses occurring during transport through the sandstone aquifer underlying the study site. © 2013 Elsevier B.V.
Kurosawa K.,Massachusetts Institute of Technology |
Radek A.,Massachusetts Institute of Technology |
Radek A.,Institute of Bio and Geosciences |
Plassmeier J.K.,Massachusetts Institute of Technology |
Sinskey A.J.,Massachusetts Institute of Technology
Biotechnology for Biofuels | Year: 2015
Background: Glycerol generated during renewable fuel production processes is potentially an attractive substrate for the production of value-added materials by fermentation. An engineered strain MITXM-61 of the oleaginous bacterium Rhodococcus opacus produces large amounts of intracellular triacylglycerols (TAGs) for lipid-based biofuels on high concentrations of glucose and xylose. However, on glycerol medium, MITXM-61 does not produce TAGs and grows poorly. The aim of the present work was to construct a TAG-producing R. opacus strain capable of high-cell-density cultivation at high glycerol concentrations. Results: An adaptive evolution strategy was applied to improve the conversion of glycerol to TAGs in R. opacus MITXM-61. An evolved strain, MITGM-173, grown on a defined medium with 16 g L-1 glycerol, produced 2.3 g L-1 of TAGs, corresponding to 40.4% of the cell dry weight (CDW) and 0.144 g g-1 of TAG yield per glycerol consumed. MITGM-173 was able to grow on high concentrations (greater than 150 g L-1) of glycerol. Cultivated in a medium containing an initial concentration of 20 g L-1 glycerol, 40 g L-1 glucose, and 40 g L-1 xylose, MITGM-173 was capable of simultaneously consuming the mixed substrates and yielding 13.6 g L-1 of TAGs, representing 51.2% of the CDM. In addition, when 20 g L-1 glycerol was pulse-loaded into the culture with 40 g L-1 glucose and 40 g L-1 xylose at the stationary growth phase, MITGM-173 produced 14.3 g L-1 of TAGs corresponding to 51.1% of the CDW although residual glycerol in the culture was observed. The addition of 20 g L-1 glycerol in the glucose/xylose mix resulted in a TAG yield per glycerol consumed of 0.170 g g-1 on the initial addition and 0.279 g g-1 on the pulse addition of glycerol. Conclusion: We have generated a TAG-producing R. opacus MITGM-173 strain that shows significantly improved glycerol utilization in comparison to the parental strain. The present study demonstrates that the evolved R. opacus strain shows significant promise for developing a cost-effective bioprocess to generate advanced renewable fuels from mixed sugar feedstocks supplemented with glycerol. © 2015 Kurosawa et al.; licensee BioMed Central.
Nischwitz V.,Central Institute for Engineering |
Gottselig N.,Institute of Bio and Geosciences |
Missong A.,Institute of Bio and Geosciences |
Meyn T.,Norwegian University of Science and Technology |
Klumpp E.,Institute of Bio and Geosciences
Journal of Analytical Atomic Spectrometry | Year: 2016
Reliable and efficient analytical techniques are required for quantitative size-resolved carbon determination of nanoparticles and colloids in complex sample matrices due to the key role of carbon in biological and environmental processes. Field flow fractionation (FFF) online with inductively coupled plasma mass spectrometry (ICP-MS) is a powerful technique for identification and quantification of particle bound metals, but has not been applied for quantitative determination of particulate carbon, yet, due to several challenges. Therefore, our study explores the potential of online particulate carbon detection by ICP-MS to overcome limitations of previously used UV detection or offline total organic carbon measurements. A novel organic carbon detector (OCD) was used as independent sensitive carbon detector to validate the ICP-MS results. Basic validation of organic carbon detection by offline quadrupole and sector-field ICP-MS was performed for fresh water samples using OCD as reference achieving recoveries of 107 ± 16% with Q-ICP-MS and 122 ± 22% with SF-ICP-MS. Limits of detection were 0.6 mg L-1 for Q-ICP-MS, 0.3 mg L-1 for SF-ICP-MS and 0.04 mg L-1 for OCD. The main focus was on comparison of FFF-ICP-MS and FFF-OCD for quantification of particulate carbon in fresh water samples, soil extracts as well as in bovine serum albumin (BSA) as candidate reference standard. Recoveries obtained by FFF-Q-ICP-MS with a flow-injection calibration approach were in a range from 90 to 113% for replicate analyses of fresh water samples compared to FFF-OCD and from 87 to 107% with an alternative post-channel calibration strategy. © The Royal Society of Chemistry 2016.
Wasson A.,CSIRO |
Bischof L.,CSIRO |
Zwart A.,CSIRO |
Watt M.,CSIRO |
Watt M.,Institute of Bio and Geosciences
Journal of Experimental Botany | Year: 2016
Root architecture traits are a target for pre-breeders. Incorporation of root architecture traits into new cultivars requires phenotyping. It is attractive to rapidly and directly phenotype root architecture in the field, avoiding laboratory studies that may not translate to the field. A combination of soil coring with a hydraulic push press and manual core-break counting can directly phenotype root architecture traits of depth and distribution in the field through to grain development, but large teams of people are required and labour costs are high with this method. We developed a portable fluorescence imaging system (BlueBox) to automate root counting in soil cores with image analysis software directly in the field. The lighting system was optimized to produce high-contrast images of roots emerging from soil cores. The correlation of the measurements with the root length density of the soil cores exceeded the correlation achieved by human operator measurements (R 2=0.68 versus 0.57, respectively). A BlueBox-equipped team processed 4.3 cores/hour/person, compared with 3.7 cores/hour/person for the manual method. The portable, automated in-field root architecture phenotyping system was 16% more labour efficient, 19% more accurate, and 12% cheaper than manual conventional coring, and presents an opportunity to directly phenotype root architecture in the field as part of pre-breeding programs. The platform has wide possibilities to capture more information about root health and other root traits in the field. © 2016 The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.
Gruenberger A.,Institute of Bio and Geosciences
Journal of visualized experiments : JoVE | Year: 2013
In this protocol the fabrication, experimental setup and basic operation of the recently introduced microfluidic picoliter bioreactor (PLBR) is described in detail. The PLBR can be utilized for the analysis of single bacteria and microcolonies to investigate biotechnological and microbiological related questions concerning, e.g. cell growth, morphology, stress response, and metabolite or protein production on single-cell level. The device features continuous media flow enabling constant environmental conditions for perturbation studies, but in addition allows fast medium changes as well as oscillating conditions to mimic any desired environmental situation. To fabricate the single use devices, a silicon wafer containing sub micrometer sized SU-8 structures served as the replication mold for rapid polydimethylsiloxane casting. Chips were cut, assembled, connected, and set up onto a high resolution and fully automated microscope suited for time-lapse imaging, a powerful tool for spatio-temporal cell analysis. Here, the biotechnological platform organism Corynebacterium glutamicum was seeded into the PLBR and cell growth and intracellular fluorescence were followed over several hours unraveling time dependent population heterogeneity on single-cell level, not possible with conventional analysis methods such as flow cytometry. Besides insights into device fabrication, furthermore, the preparation of the preculture, loading, trapping of bacteria, and the PLBR cultivation of single cells and colonies is demonstrated. These devices will add a new dimension in microbiological research to analyze time dependent phenomena of single bacteria under tight environmental control. Due to the simple and relatively short fabrication process the technology can be easily adapted at any microfluidics lab and simply tailored towards specific needs.
Kienel U.,Helmholtz Center Potsdam |
Vos H.,Institute for Energy Research of Germany |
Dulski P.,Helmholtz Center Potsdam |
Lucke A.,Institute of Bio and Geosciences |
And 3 more authors.
Journal of Paleolimnology | Year: 2013
Paleolimnological data from varved sediments in Lake Holzmaar (Eifel, Germany) were combined with documentary data on human activities, long-term data from the Historical Climate Database (HISKLID) for Germany and with recent monitoring data to evaluate changes in deposition that arose from climatic and human influences. The sediment data included seasonal layer thickness in an established varve chronology (1608-1942 AD), subannual chemical element counts, and multiannual organic matter data (TOC, TN, δ13Corg), all combined on an annual scale. Indicators for detritus deposition (lithogenic element counts and detritus layers) determined the first principal component (PC1) of the sediment data. This detritus PC1 was compared to the first PCs of the seasonal precipitation and temperature from HISKLID. While no relation was found to precipitation, the correlation with the temperature PC1 determined by spring to fall temperatures was significant. From 1608 to 1870, a positive correlation of the PCs suggests an increase of detritus deposition in the lake center with increasing non-winter temperatures. These may be linked by lake-internal sediment redeposition that increases when the periods of winter stratification become shorter and that of lake circulation longer. The detritus deposition is modulated by external detritus input depending on the intensity of erosion-conducive land use (wood pasture, wood cutting, and rotational slash-and-burn cultivation). Detritus input diminished when land use slowed down with population decrease as the consequence of plague epidemics, warfare and emigration. After 1870, forest regeneration and improving agricultural practices led to a stabilization of the catchment. Erosion and detritus deposition decreased progressively. The negative correlation of detritus deposition with the gradually increasing temperature presumably mimics a cause-effect relation, although a link with decreasing freeze-thaw action is possible. The modernization of agriculture proceeded with manuring and fertilizing, which caused an increase of lake productivity as indicated by summer blooms of diatoms with enhanced nutrient demand, increased δ13Corg values and sulfur concentrations. Within this well established data base we found combinations of criteria that may be used to deduce natural climatic or anthropogenic influences. The quantitative attribution of these influences remains a challenging task in paleolimnology because their interaction makes the detection of linking mechanisms difficult even at high degree of detail and the processes themselves remain debatable. © 2013 Springer Science+Business Media Dordrecht.
Baumgart M.,Institute of Bio and Geosciences |
Frunzke J.,Institute of Bio and Geosciences
FEMS Microbiology Letters | Year: 2015
Manganese is an important trace element required as an enzyme cofactor and for protection against oxidative stress. In this study, we characterized the DtxR-type transcriptional regulator MntR (cg0741) of Corynebacterium glutamicum ATCC 13032 as a manganese-dependent repressor of the predicted ZIP family metal transporter Cg1623. Comparative transcriptome analysis of a ±mntR strain and the wild type led to the identification of cg1623 as potential target gene of MntR which was about 50-fold upregulated when cells were grown in glucose minimal medium. Using electrophoretic mobility shift assays, a conserved 18 bp inverted repeat (TGTTCAATGCGTTGAACA) was identified as binding motif of MntR in the cg1623 promoter and confirmed by mutational analysis. Promoter fusion of Pcg1623 to eyfp confirmed that the MntR-dependent repression is only abolished in the absence of manganese. However, neither deletion of mntR nor cg1623 resulted in a significant growth phenotype in comparison to the wild type-strongly suggesting the presence of further manganese uptake and efflux systems in C. glutamicum. The control of cg1623 by the DtxR-type regulator MntR represents the first example of a predicted ZIP family protein that is regulated in a manganese-dependent manner in bacteria. © FEMS 2014.