Biomimetic Dehydrogenation of Non-Conventional Lignin Monomers on Cellulose Ferulate Interfaces.

Cellulose ferulate, synthesized by Mitsunobu reaction, is shaped into thin films and also used as an aqueous dispersion to perform artificial lignin polymerization on anchor groups. This biomimetic approach is carried out in a Quartz crystal microbalance with a dissipation monitoring (QCM-D) device to enable online monitoring of the dehydrogenation, applying H2O2 and adsorbed horseradish peroxidase (HRP). The systematic use of phenylpropanoids with different oxidation states, i.e., ferulic acid, coniferyl aldehyde, coniferyl alcohol, and eugenol allowed to conclude structure-property relationships. Both the deposited material, as well as the surface roughness increased with the hydrophobicity of the monomers. Beyond surface characterizations, py-GC-MS, HSQC NMR spectroscopy and Size exclusion chromatography (SEC) measurements revealed the linkage types ß-ß, ß-5, 5-5, and ß-O-4, as well as the oligomeric character of the dehydrogenation products. All samples possessed an antibacterial activity against B. subtilis and can be used in the field of antimicrobial biomaterials.

Slow dynamics and nonergodicity of the bosonic quantum East model in the semiclassical limit.

We study the unitary dynamics of the bosonic quantum East model, a kinetically constrained lattice model which generalizes the quantum East model to arbitrary occupation per site. We consider the semiclassical limit of large (but finite) site occupancy so that the dynamics is approximated by an evolution equation of the Gross-Pitaevskii kind. This allows us to numerically study in detail system sizes of hundreds of sites. Like in the spin-1/2 case, we find two dynamical phases, an active one of fast thermalization and an inactive one of slow relaxation and the absence of ergodicity on numerically accessible timescales. The location of this apparent ergodic to nonergodic transition coincides with the localization transition of the ground state. We further characterize states which are nonergodic on all timescales in the otherwise ergodic regime.

Fate of a biodegradable plastic in forest soil: Dominant tree species and forest types drive changes in microbial community assembly, influence the composition of plastisphere, and affect poly(butylene succinate-co-adipate) degradation.

Poly(butylene succinate-co-adipate) (PBSA) degradation and its plastisphere microbiome in cropland soils have been studied; however, such knowledge is limited in the case of forest ecosystems. In this context, we investigated: i) the impact of forest types (conifer and broadleaved forests) on the plastisphere microbiome and its community assembly, ii) their link to PBSA degradation, and iii) the identities of potential microbial keystone taxa. We determined that forest type significantly affected microbial richness (F = 5.26-9.88, P = 0.034 to 0.006) and fungal community composition (R2 = 0.38, P = 0.001) of the plastisphere microbiome, whereas its effects on microbial abundance and bacterial community composition were not significant. The bacterial community was governed by stochastic processes (mainly homogenizing dispersal), whereas the fungal community was driven by both stochastic and deterministic processes (drift and homogeneous selection). The highest molar mass loss was found for PBSA degraded under Pinus sylvestris (26.6 ± 2.6 to 33.9 ± 1.8 % (mean ± SE) at 200 and 400 days, respectively), and the lowest molar mass loss was found under Picea abies (12.0 ± 1.6 to 16.0 ± 0.5 % (mean ± SE) at 200 and 400 days, respectively). Important fungal PBSA decomposers (Tetracladium) and atmospheric dinitrogen (N2)-fixing bacteria (symbiotic: Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Methylobacterium and non-symbiotic: Mycobacterium) were identified as potential keystone taxa. The present study is among the first to determine the plastisphere microbiome and its community assembly processes associated with PBSA in forest ecosystems. We detected consistent biological patterns in the forest and cropland ecosystems, indicating a potential mechanistic interaction between N2-fixing bacteria and Tetracladium during PBSA biodegradation.

Aerosol emissions from a marine diesel engine running on different fuels and effects of exhaust gas cleaning measures.

The emissions of marine diesel engines have gained both global and regional attentions because of their impact on human health and climate change. To reduce ship emissions, the International Maritime Organization capped the fuel sulfur content of marine fuels. Consequently, either low-sulfur fuels or additional exhaust gas cleaning devices for the reduction in sulfur dioxide (SO2) emissions became mandatory. Although a wet scrubber reduces the amount of SO2 significantly, there is still a need to consider the reduction in particle emissions directly. We present data on the particle removal efficiency of a scrubber regarding particle number and mass concentration with different marine fuel types, marine gas oil, and two heavy fuel oils (HFOs). An open-loop sulfur scrubber was installed in the exhaust line of a marine diesel test engine. Fine particulate matter was comprehensively characterized in terms of its physical and chemical properties. The wet scrubber led up to a 40% reduction in particle number, whereas a reduction in particle mass emissions was not generally determined. We observed a shift in the size distribution by the scrubber to larger particle diameters when the engine was operated on conventional HFOs. The reduction in particle number concentrations and shift in particle size were caused by the coagulation of soot particles and formation/growing of sulfur-containing particles. Combining the scrubber with a wet electrostatic precipitator as an additional abatement system showed a reduction in particle number and mass emission factors by >98%. Therefore, the application of a wet scrubber for the after-treatment of marine fuel oil combustion will reduce SO2 emissions, but it does not substantially affect the number and mass concentration of respirable particulate matters. To reduce particle emission, the scrubber should be combined with additional abatement systems.

A Solvent-Free Approach to Crosslinked Hydrophobic Polymeric Coatings on Paper Using Vegetable Oil.

Hydrophobic coatings are of utmost importance for many applications of paper-based materials. However, to date, most coating methods demand vast amounts of chemicals and solvents. Frequently, fossil-based coating materials are being used and multiple derivatization reactions are often required to obtain desired performances. In this work, we present a solvent-free paper-coating process, where olive oil as the main biogenic component is being used to obtain a hydrophobic barrier on paper. UV-induced thiol-ene photocrosslinking of olive oil was pursued in a solvent-free state at a wavelength of 254 nm without addition of photoinitiator. Optimum reaction conditions were determined in advance using oleic acid as a model compound. Paper coatings based on olive oil crosslinked by thiol-ene reaction reach water contact angles of up to 120°. By means of Fourier transform infrared spectroscopy and differential scanning calorimetry, a successful reaction and the formation of a polymer network within the coating can be proven. These results show that click-chemistry strategies can be used to achieve hydrophobic polymeric paper coatings while keeping the amount of non-biobased chemicals and reaction steps at a minimum.

Nitrogen fixing bacteria facilitate microbial biodegradation of a bio-based and biodegradable plastic in soils under ambient and future climatic conditions.

We discovered a biological mechanism supporting microbial degradation of bio-based poly(butylene succinate-co-adipate) (PBSA) plastic in soils under ambient and future climates. Here, we show that nitrogen-fixing bacteria facilitate the microbial degradation of PBSA by enhancing fungal abundance, accelerating plastic-degrading enzyme activities, and shaping/interacting with plastic-degrading fungal communities.

Back to the Future: Decomposability of a Biobased and Biodegradable Plastic in Field Soil Environments and Its Microbiome under Ambient and Future Climates.

Decomposition by microorganisms of plastics in soils is almost unexplored despite the fact that the majority of plastics released into the environment end up in soils. Here, we investigate the decomposition process and microbiome of one of the most promising biobased and biodegradable plastics, poly(butylene succinate-co-adipate) (PBSA), under field soil conditions under both ambient and future predicted climates (for the time between 2070 and 2100). We show that the gravimetric and molar mass of PBSA is already largely reduced (28-33%) after 328 days under both climates. We provide novel information on the PBSA microbiome encompassing the three domains of life: Archaea, Bacteria, and Eukarya (fungi). We show that PBSA begins to decompose after the increase in relative abundances of aquatic fungi (Tetracladium spp.) and nitrogen-fixing bacteria. The PBSA microbiome is distinct from that of surrounding soils, suggesting that PBSA serves as a new ecological habitat. We conclude that the microbial decomposition process of PBSA in soil is more complex than previously thought by involving interkingdom relationships, especially between bacteria and fungi.

Entrapment of Hydrophobic Biocides into Cellulose Acetate Nanoparticles by Nanoprecipitation.

This contribution reports an efficient method for the production and use of biocide-loaded cellulose acetate nanoparticles. As well-known model biocides 4-Hexylresorcinol and Triclosan were used for in situ nanoparticle loading during a nanoprecipitation process. We show that the nanoparticle size can be well-controlled by variation of the cellulose acetate concentration during nanoprecipitation. Apart from strong evidence suggesting cellulose acetate particle formation according to a nucleation-aggregation mechanism, we further show that the biocide loading of the particles occurs by a diffusion process and not via co-precipitation. The quantity of particle loading was analyzed by 1H-NMR spectroscopy of re-dissolved nanoparticles, and it was observed that a decisive factor for high packaging efficiency is the use of a biocide with low water solubility and high hydrophobicity. SEM studies showed no influence on the particle morphology or size by both biocides 4-Hexylresorcinol and Triclosan. Finally, an aqueous nanoparticle dispersion can be coated onto model paper sheets to yield pronounced antimicrobial surface-properties. Nanoparticles loaded with the biocide Triclosan showed a high antimicrobial activity against Bacillus subtilis, a cellulase producing bacteria, if applied to model paper substrates, even at extremely low coating weights of 1-5 g/m2, respectively. Additional long-term efficacy renders these nanoparticles ideal for various applications.

Exploring the potential of comparative de novo transcriptomics to classify Saccharomyces brewing yeasts.

In this work the potential of comparative transcriptomics was explored of Saccharomyces (S.) cerevisiae and S. pastorianus for their discrimination. This way an alternative should be demonstrated to comparative genomics, which can be difficult as a result of their aneuoploid genomes composed of mosaics of the parental genomes. Strains were selected according to their application in beer brewing, i.e. top and bottom fermenting yeasts. Comparative transcriptomics was performed for four strains each of commercially available S. cerevisiae (top fermenting) and Saccharomyces pastorianus (bottom fermenting) brewing yeasts grown at two different temperatures to mid-exponential growth phase. A non-reference based approach was chosen in the form of alignment against a de novo assembled brewery-associated pan transcriptome to exclude bias introduced by manual selection of reference genomes. The result is an analysis workflow for self-contained comparative transcriptomics of Saccharomyces yeasts including, but not limited to, the analysis of core and accessory gene expression, functional analysis and metabolic classification. The functionality of this workflow is demonstrated along the principal differentiation of accessory transcriptomes of S. cerevisiae versus S. pastorianus strains. Hence, this work provides a concept enabling studies under different brewing conditions.

Metatranscriptomic analysis of modified atmosphere packaged poultry meat enables prediction of Brochothrix thermosphacta and Carnobacterium divergens in situ metabolism.

In this study, in situ-expressed metabolic routes of Brochothrix (B.) thermosphacta and Carnobacterium (C.) divergens were evaluated based on a metatranscriptomic dataset from bacteria growing on MAP chicken meat (O2/CO2; N2/CO2). Both species exhibited no (C. divergens) or minor transcription regulation (B. thermosphacta) within their main metabolic routes in response to different atmospheres. Both employ pathways related to glucose and ribose. Gluconeogenesis from lipid-borne glycerol is active in the progressing lack of carbohydrates. Pyruvate fates in both species comprise lactate, ethanol, acetate, CO2, formate, C4-compounds and H2O2 (only B. thermosphacta). Both species express genes for a minimal aerobic respiratory chain, but do not possess the genetic setting for a functional citric acid cycle. While products of carbohydrate and glycerol metabolism display mild to medium sensorial off-characteristics, predicted end products of their amino acid metabolism comprise, e.g., isobutyrate and isovalerate (B. thermosphacta) or cadaverine and tyramine (C. divergens) as potent spoilage compounds.

Prediction of in situ metabolism of photobacteria in modified atmosphere packaged poultry meat using metatranscriptomic data.

Modified atmosphere packaging (MAP) is widely used in food industry to extend the microbiological shelf life of meat. Common CO2-containing gas atmospheres for poultry meat packaging are either nearly O2-free or high O2 MAPs. In this work, we compared spoilage microbiota of skinless chicken breast in CO2/O2 (30/70%) and CO2/N2 (30/70%) MAP, which are culturable with conventional methods and identified isolates by MALDI-TOF MS. These data were compared to metatranscriptome sequencing enabling a culture-independent overview on the composition of microbiota at species level. While typical MAP meat spoilers were confirmed in the transcriptomic approach, we also found high numbers of transcripts mapping to Photobacterium spp. sequences in these samples. As photobacteria were recently shown to occur in different MAP and vacuum packaged meats, we used the respective part of the metatranscriptomic data for prediction of Photobacterium spp. major metabolic routes in situ, upon growth in MAP poultry meat. It is predicted that they employ similar metabolism in both atmospheres: In the lack of carbohydrates upon meat spoilage, the pyruvate pool is filled via glycerol originating from lipolysis and amino acid conversions. From the pyruvate pool, gluconeogenesis is fed enabling cell wall biosynthesis and growth as well as catabolism to lactate and other metabolites, or anaplerosis towards the citric acid cycle. Production is predicted of several biogenic amines including tyramine and cadaverine, enabling generation of proton motive force. Taken together, photobacteria express metabolic pathways upon growth on meat, which should lead to compounds overlapping with those of known potent meat spoilers.

Comparative genomics of Lactobacillus sakei supports the development of starter strain combinations.

Strains of Lactobacillus sakei can be isolated from a variety of sources including meat, fermented sausages, sake, sourdough, sauerkraut or kimchi. Selected strains are widely used as starter cultures for sausage fermentation. Recently we have demonstrated that control about the lactic microbiota in fermenting sausages is achieved rather by pairs or strain sets than by single strains. In this work we characterized the pan genome of L. sakei to enable exploitation of the genomic diversity of L. sakei for the establishment of assertive starter strain sets. We have established the full genome sequences of nine L. sakei strains from different sources of isolation and included in the analysis the genome of L. sakei 23K. Comparative genomics revealed an accessory genome comprising about 50% of the pan genome and different lineages of strains with no relation to their source of isolation. Group and strain specific differences could be found, which namely referred to agmatine and citrate metabolism. The presence of genes encoding metabolic pathways for fructose, sucrose and trehalose as well as gluconate in all strains suggests a general adaptation to plant/sugary environments and a life in communities with other genera. Analysis of the plasmidome did not reveal any specific mechanisms of adaptation to a habitat. The predicted differences of metabolic settings enable prediction of partner strains, which can occupy the meat environment to a large extent and establish competitive exclusion of autochthonous microbiota. This may assist the development of a new generation of meat starter cultures containing L. sakei strains.

Label-free quantitative proteomic analysis reveals the lifestyle of Lactobacillus hordei in the presence of Sacchromyces cerevisiae.

Water kefir is a fermented beverage, which is traditionally prepared from sucrose, kefir grains, dried or fresh fruits, and water. L. hordei and S. cerevisiae are isolated as predominant and stable species of lactic acid bacteria and yeasts, respectively. In this study we demonstrate that label free quantitative proteomics is useful to study microbial interaction along the response of co-cultivated L. hordei TMW 1.1822 in the presence of S. cerevisiae TMW 3.221 as compared with their single cultures in a water kefir model. It is shown and L. hordei responds to S. cerevisiae in many respects revealing a mutualistic relationship. The data suggest that L. hordei responds to the presence of S. cerevisiae with adjustment of intracellular redox reactions controlled of proteins, which are part of Rex regulons and proteins involved in the glycolytic pathway and energy fermentation. An NADH, H+-driven metabolic switch to preferential production of butanediol instead of acetate or lactate, and up-regulation of arginine deiminase, alleviated acid stress and concomitantly protected S. cerevisiae against an acidic environment, which L. hordei generated in single culture. Moreover, the data suggest that the presence of S. cerevisiae in the nitrogen and fatty acids limited environment of the water kefir facilitated and improved the growth of L. hordei by delivering gluconate, fructose, amino acids, fatty acids or substrates for their biosynthesis. Up-regulation of the OppABCDF peptide transport and enzymes involved in amino acid metabolism indicates enhanced peptide uptake, as well as cross-feeding of L. hordei by glutamine, glutamate, histidine, tryptophan, methionine, proline, tryptophan delivered by S. cerevisiae.

Lifestyle of Lactobacillus hordei isolated from water kefir based on genomic, proteomic and physiological characterization.

Water kefir is a traditional fermented beverage made from sucrose, water, kefir granules, dried or fresh fruits. In our water kefir granules, Lactobacillus (L.) hordei is one of the predominant lactic acid bacteria (LAB) species of this presumed symbiotic consortium. It faces abundant sucrose versus limitation of amino- and fatty acids in an acidic environment. Sequencing of the genome of L. hordei TMW 1.1822 revealed one chromosome plus three plasmids. The size of the chromosome was 2.42 Mbp with a GC content of 35% GC and 2461 predicted coding sequences. Furthermore, we identified 1474 proteins upon growth on water kefir medium. Metabolic prediction revealed all enzymes required for the glycolytic Embden-Meyerhof (EMP) and phosphoketolase (PKP) pathways. Genes encoding all enzymes involved in citrate, pyruvate and mannitol metabolism are present. Moreover, it was confirmed that L. hordei is prototrophic for 11 amino acids and auxotrophic for 6 amino acids when combining putative biosynthesis pathways for amino acids with physiological characterization. Still, for glycine, serine and methionine no sure auxotype could be determined. The OppABCDF peptide transport system is complete, and 13 genes encoding peptidases are present. The arginine deiminase system, was predicted to be complete except for carbamate kinase, thus enabling neutralization reactions via ammonium formation but no additional energy generation. Taken together our findings enable prediction of the L. hordei lifestyle in water kefir: Abundant sucrose is consumed directly via parallel EMP and PK pathways and is also extracellularly converted to dextran and fructose by a glucansucrase, leaving fructose as additional carbon source. Essential amino acids (in the form of peptides) and citrate are acquired from fruits. In the lack of FabB unsaturated fatty acids are synthesized by predicted alternative enzymes. Formation of acetoin and diacetyl as well as arginine conversion reactions enable acidification limitation. Other members of the water kefir consortium (yeasts, acetic acid bacteria) likely facilitate or support growth of L. hordei by delivering gluconate, mannitol, amino- and fatty acids and vitamins.

Comparative Genomics of Lactobacillus brevis Reveals a Significant Plasmidome Overlap of Brewery and Insect Isolates.

Lactobacillus (L.) brevis represents a versatile, ubiquitistic species of lactic acid bacteria, occurring in various foods, as well as plants and intestinal tracts. The ability to deal with considerably differing environmental conditions in the respective ecological niches implies a genomic adaptation to the particular requirements to use it as a habitat beyond a transient state. Given the isolation source, 24 L. brevis genomes were analyzed via comparative genomics to get a broad view of the genomic complexity and ecological versatility of this species. This analysis showed L. brevis being a genetically diverse species possessing a remarkably large pan genome. As anticipated, it proved difficult to draw a correlation between chromosomal settings and isolation source. However, on plasmidome level, brewery- and insect-derived strains grouped into distinct clusters, referable to a noteworthy gene sharing between both groups. The brewery-specific plasmidome is characterized by several genes, which support a life in the harsh environment beer, but 40% of the brewery plasmidome were found in insect-derived strains as well. This suggests a close interaction between these habitats. Further analysis revealed the presence of a truncated horC cluster version in brewery- and insect-associated strains. This disproves horC, the major contributor to survival in beer, as brewery isolate specific. We conclude that L. brevis does not perform rigorous chromosomal changes to live in different habitats. Rather it appears that the species retains a certain genetic diversity in the plasmidome and meets the requirements of a particular ecological niche with the acquisition of appropriate plasmids.

Characterization of ß-glucan formation by Lactobacillus brevis TMW 1.2112 isolated from slimy spoiled beer.

Despite several hurdles, which hinder bacterial growth in beer, certain bacteria are still able to spoil beer. One type of spoilage is characterized by an increased viscosity and slimy texture caused by exopolysaccharide (EPS) formation of lactic acid bacteria (LAB). In this study, we characterize for the first time EPS production in a beer-spoiling strain (TMW 1.2112) of Lactobacillus brevis, a species commonly involved in beer spoilage. The strain's growth dynamics were assessed and we found an increased viscosity or ropiness in liquid or on solid media, respectively. Capsular polysaccharides (CPS) and released EPS from the cells or supernatant, respectively, were analyzed via NMR spectroscopy and methylation analysis. Both are identical ß-(1→3)-glucans, which are ramified with ß-glucose residues at position O2. Therefore, we assume that this EPS is mainly produced as CPS and partially released into the surrounding medium, causing viscosity of e.g. beer. CPS formation was confirmed via an agglutination test. A plasmid-located glycosyltransferase-2 was found as responsible for excess ß-glucan formation, chromosomal glucanases were proposed for its degradation. The glycosyltransferase-2 gene could also be specifically identified in beer-spoiling, slime-producing Lactobacillus rossiae and Lactobacillus parabuchneri strains, suggesting it as promising marker gene for the early detection of ß-glucan-producing Lactobacilli in breweries.

Quantitative Proteomics for the Comprehensive Analysis of Stress Responses of Lactobacillus paracasei subsp. paracasei F19.

Lactic acid bacteria are broadly employed as starter cultures in the manufacture of foods. Upon technological preparation, they are confronted with drying stress that amalgamates numerous stress conditions resulting in losses of fitness and survival. To better understand and differentiate physiological stress responses, discover general and specific markers for the investigated stress conditions, and predict optimal preconditioning for starter cultures, we performed a comprehensive genomic and quantitative proteomic analysis of a commonly used model system, Lactobacillus paracasei subsp. paracasei TMW 1.1434 (isogenic with F19) under 11 typical stress conditions, including among others oxidative, osmotic, pH, and pressure stress. We identified and quantified >1900 proteins in triplicate analyses, representing 65% of all genes encoded in the genome. The identified genes were thoroughly annotated in terms of subcellular localization prediction and biological functions, suggesting unbiased and comprehensive proteome coverage. In total, 427 proteins were significantly differentially expressed in at least one condition. Most notably, our analysis suggests that optimal preconditioning toward drying was predicted to be alkaline and high-pressure stress preconditioning. Taken together, we believe the presented strategy may serve as a prototypic example for the analysis and utility of employing quantitative-mass-spectrometry-based proteomics to study bacterial physiology.

Multiple Genome Sequences of Exopolysaccharide-Producing, Brewery-Associated Lactobacillus brevis Strains.

Lactobacillus brevis represents one of the most relevant beer-spoiling bacteria. Besides strains causing turbidity and off flavors upon growth and metabolite formation, this species also comprises strains that produce exopolysaccharides (EPSs), which increase the viscosity of beer. Here, we report the complete genome sequences of three EPS-producing, brewery-associated L. brevis strains.

Multiple Genome Sequences of Lactobacillus plantarum Strains.

We report here the genome sequences of four Lactobacillus plantarum strains which vary in surface hydrophobicity. Bioinformatic analysis, using additional genomes of Lactobacillus plantarum strains, revealed a possible correlation between the cell wall teichoic acid-type and cell surface hydrophobicity and provide the basis for consecutive analyses.

Multiple Genome Sequences of Heteropolysaccharide-Forming Acetic Acid Bacteria.

We report here the complete genome sequences of the acetic acid bacteria (AAB) Acetobacter aceti TMW 2.1153, A. persici TMW 2.1084, and Neoasaia chiangmaiensis NBRC 101099, which secrete biotechnologically relevant heteropolysaccharides (HePSs) into their environments. Upon genome sequencing of these AAB strains, the corresponding HePS biosynthesis pathways were identified.