Metabolic profiling of rhizobacteria Serratia plymuthica and Bacillus subtilis revealed intra- and interspecific differences and elicitation of plipastatins and short peptides due to co-cultivation

Rhizobacteria live in diverse and dynamic communities having a high impact on plant growth and development. Due to the complexity of the microbial communities and the difficult accessibility of the rhizosphere, investigations of interactive processes within this bacterial network are challenging. In order to better understand causal relationships between individual members of the microbial community of plants, we started to investigate the inter- and intraspecific interaction potential of three rhizobacteria, the S. plymuthica isolates 4Rx13 and AS9 and B. subtilis B2g, using high resolution mass spectrometry based metabolic profiling of structured, low-diversity model communities. We found that by metabolic profiling we are able to detect metabolite changes during cultivation of all three isolates. The metabolic profile of S. plymuthica 4Rx13 differs interspecifically to B. subtilis B2g and surprisingly intraspecifically to S. plymuthica AS9. Thereby, the release of different secondary metabolites represents one contributing factor of inter- and intraspecific variations in metabolite profiles. Interspecific co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g showed consistently distinct metabolic profiles compared to mono-cultivated species. Thereby, putative known and new variants of the plipastatin family are increased in the co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g. Interestingly, intraspecific co-cultivation of S. plymuthica 4Rx13 and S. plymuthica AS9 revealed a distinct interaction zone and showed distinct metabolic profiles compared to mono-cultures. Thereby, several putative short proline-containing peptides are increased in co-cultivation of S. plymuthica 4Rx13 with S. plymuthica AS9 compared to mono-cultivated strains. Our results demonstrate that the release of metabolites by rhizobacteria alters due to growth and induced by social interactions between single members of the microbial community. These results form a basis to elucidate the functional role of such interaction-triggered compounds in establishment and maintenance of microbial communities and can be applied under natural and more realistic conditions, since rhizobacteria also interact with the plant itself and many other members of plant and soil microbiota

mVOC: a database of microbial volatiles

Scents are well known to be emitted from flowers and animals. In nature, these volatiles are responsible for inter- and intra-organismic communication, e.g. attraction and defence. Consequently, they influence and improve the establishment of organisms and populations in ecological niches by acting as single compounds or in mixtures. Despite the known wealth of volatile organic compounds (VOCs) from species of the plant and animal kingdom, in the past, less attention has been focused on volatiles of microorganisms. Although fast and affordable sequencing methods facilitate the detection of microbial diseases, however, the analysis of signature or fingerprint volatiles will be faster and easier. Microbial VOCs (mVOCs) are presently used as marker to detect human diseases, food spoilage or moulds in houses. Furthermore, mVOCs exhibited antagonistic potential against pathogens in vitro, but their biological roles in the ecosystems remain to be investigated. Information on volatile emission from bacteria and fungi is presently scattered in the literature, and no public and up-to-date collection on mVOCs is available. To address this need, we have developed mVOC, a database available online at http://bioinformatics.charite.de/mvoc

mVOC 2.0: a database of microbial volatiles

Metabolic capabilities of microorganisms include the production of secondary metabolites (e.g. antibiotics). The analysis of microbial volatile organic compounds (mVOCs) is an emerging research field with huge impact on medical, agricultural and biotechnical applied and basic science. The mVOC database (v1) has grown with microbiome research and integrated species information with data on emitted volatiles. Here, we present the mVOC 2.0 database with about 2000 compounds from almost 1000 species and new features to work with the database. The extended collection of compounds was augmented with data regarding mVOC-mediated effects on plants, fungi, bacteria and (in-)vertebrates. The mVOC database 2.0 now features a mass spectrum finder, which allows a quick mass spectrum comparison for compound identification and the generation of species-specific VOC signatures. Automatic updates, useful links and search for mVOC literature are also included. The mVOC database aggregates and refines available information regarding microbial volatiles, with the ultimate aim to provide a comprehensive and informative platform for scientists working in this research field. To address this need, we maintain a publicly available mVOC database at: http://bioinformatics.charite.de/mvoc

Tailored Light Scattering through Hyperuniform Disorder in Self-Organized Arrays of High-Index Nanodisks

Arrays of nanoparticles exploited in light scattering applications commonly only feature either a periodic or a rather random arrangement of its constituents. For the periodic case, light scattering is mostly governed by the strong spatial correlations of the arrangement, expressed by the structure factor. For the random case, structural correlations cancel each other out and light scattering is mostly governed by the scattering properties of the individual scatterer, expressed by the form factor. In contrast to these extreme cases, it is shown here that hyperuniform disorder in self-organized large-area arrays of high refractive index nanodisks enables both structure and form factor to impact the resulting scattering pattern, offering novel means to tailor light scattering. The scattering response from the authors’ nearly hyperuniform interfaces can be exploited in a large variety of applications and constitutes a novel class of advanced optical materials

Correlated Disorder Substrate‐Integrated Nanodisk Scatterers for Light Extraction in Organic Light Emitting Diodes

A major loss mechanism in organic light emitting diodes (OLEDs) is the coupling of the emitter molecule light field to waveguide modes in the OLED thin film stack. In this work, a disordered 2D array of TiO$_{2}$ nanodisk scatterers is integrated into the OLED substrate to enable efficient light extraction from these waveguide modes. Fabrication of the nanodisks is based on a bottom-up, colloidal lithography technique and subsequent pattern transfer into high refractive index TiO$_{2}$ via reactive ion etching. The substrates are completed by spin-coating a polymer planarization layer before applying the OLED thin film stack. This ensures reproducible optoelectronic properties of the OLED through leaving the electrically active layers planar. Simultaneously, the nanodisks in close vicinity to the thin film stack ensure efficient out-of-plane scattering of waveguide modes. In a monochromatic OLED (center wavelength λ$_{0}$ = 520 nm), a 44.2%$_{rel}$ increase in external quantum efficiency is achieved in comparison to a device without scattering structure. An in-depth numerical analysis reveals that this significant enhancement is only partly due to the out-coupling of waveguide modes. Additional enhancement is suspected to result from out-coupling of substrate modes through scattering by the nanodisks. Further improvements to the scattering structure are numerically evaluated

Antireflective Huygens’ Metasurface with Correlated Disorder Made from High-Index Disks Implemented into Silicon Heterojunction Solar Cells

A large variety of different strategies has been proposed as alternatives to random textures to improve light coupling into solar cells. While the understanding of dedicated nanophotonic systems deepens continuously, only a few of the proposed designs are industrially accepted due to a lack of scalability. In this Article, a tailored disordered arrangement of high-index dielectric submicron-sized titanium dioxide (TiO$_{2}$) disks is experimentally exploited as an antireflective Huygens’ metasurface for standard heterojunction silicon solar cells. The disordered array is fabricated using a scalable bottom-up technique based on colloidal self-assembly that is applicable virtually irrespective of material or surface morphology of the device. We observe a broadband reduction of reflectance resulting in a relative improvement of a short-circuit current by 5.1% compared to a reference cell with an optimized flat antireflective indium tin oxide (ITO) layer. A theoretical model based on Born’s first approximation is proposed that links the current increase in the arrangement of disks expressed in terms of the structure factor S(q) of the disk array. Additionally, we discuss the optical performance of the metasurface within the framework of helicity preservation, which can be achieved at specific wavelengths for an isolated disk for illumination along the symmetry axis by tuning its dimensions. By comparison to a simulated periodic metasurface, we show that this framework is applicable in the case of the structure factor approaching zero and the disks’ arrangement becoming stealthy hyperuniform

ANALYSIS OF THE DIURNAL EXPRESSION PATTERNS OF THE TOMATO CHLOROPHYLL alb BINDING PROTEIN GENES. INFLUENCE OF LIGHT and CHARACTERIZATION OF THE GENE FAMILY *

Steady-state mRNA levels of the chlorophyll alb binding ( cab ) proteins oscillate substantially during a diurnal cycle in tomato leaves. This accumulation pattern is also observed in complete darkness, supporting the hypothesis that the expression of cab genes is at least partially regulated by an endogenous rhythm (“biological clock”). The amplitude of the cab mRNA accumulation is dependent on the duration of illumination and the circadian phase in which light was applied to the tomato plants. These results at the molecular level correlate well with the photoperiodic phenomenon. The characterization of the expression pattern of individual members of the cab gene family was attempted. Distinct primer extension products were detected using specific oligonucleotides homologous to the cab 1, cab 4, cab 5 and cab 8 genes. Based on this analysis the transcription start sites of these genes were determined to be between position -70 and -9 upstream of the ATG codon. During the diurnal cycle the cab 1 and cab 4 genes exhibit the same expression pattern; no transcripts detected at 3 and 6 a.m., maximum mRNA levels were measured at noon and decreasing levels in the afternoon.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74852/1/j.1751-1097.1990.tb01752.x.pd

Strategy for tailoring the size distribution of nanospheres to optimize rough backreflectors of solar cells

We study the light-trapping properties of surface textures generated by a bottom-up approach, which utilizes monolayers of densely deposited nanospheres as a template. We demonstrate that just allowing placement disorder in monolayers from identical nanospheres can already lead to a significant boost in light-trapping capabilities. Further absorption enhancement can be obtained by involving an additional nanosphere size species. We show that the Power Spectral Density provides limited correspondence to the diffraction pattern and in turn to the short-circuit current density enhancement for large texture modulations. However, in predicting the optimal nanosphere size distribution, we demonstrate that full-wave simulations of just a c-Si semi-infinite halfspace at a single wavelength in the range where light trapping is of main importance is sufficient to provide an excellent estimate. The envisioned bottom-up approach can thus reliably provide good light-trapping surface textures even with simple nanosphere monolayer templates defined by a limited number of control parameters: two nanosphere radii and their occurrence probability

SuperScent—a database of flavors and scents

Volatiles are efficient mediators of chemical communication acting universally as attractant, repellent or warning signal in all kingdoms of life. Beside this broad impact volatiles have in nature, scents are also widely used in pharmaceutical, food and cosmetic industries, so the identification of new scents is of great industrial interest. Despite this importance as well as the vast number and diversity of volatile compounds, there is currently no comprehensive public database providing information on structure and chemical classification of volatiles. Therefore, the database SuperScent was established to supply users with detailed information on the variety of odor components. The version of the database presented here comprises the 2D/3D structures of approximately 2100 volatiles and around 9200 synonyms as well as physicochemical properties, commercial availability and references. The volatiles are classified according to their origin, functionality and odorant groups. The information was extracted from the literature and web resources. SuperScent offers several search options, e.g. name, Pubchem ID number, species, functional groups, or molecular weight. SuperScent is available online at: http://bioinformatics.charite.de/superscent