Guided cobamide biosynthesis for heterologous production of reductive dehalogenases

Cobamides (Cbas) are essential cofactors of reductive dehalogenases (RDases) in organohalide-respiring bacteria (OHRB). Changes in the Cba structure can influence RDase function. Here, we report on the cofactor versatility or selectivity of Desulfitobacterium RDases produced either in the native organism or heterologously. The susceptibility of Desulfitobacterium hafniense strain DCB-2 to guided Cba biosynthesis (i.e. incorporation of exogenous Cba lower ligand base precursors) was analysed. Exogenous benzimidazoles, azabenzimidazoles and 4,5-dimethylimidazole were incorporated by the organism into Cbas. When the type of Cba changed, no effect on the turnover rate of the 3-chloro-4-hydroxy-phenylacetate-converting enzyme RdhA6 and the 3,5-dichlorophenol-dehalogenating enzyme RdhA3 was observed. The impact of the amendment of Cba lower ligand precursors on RDase function was also investigated in Shimwellia blattae, the Cba producer used for the heterologous production of Desulfitobacterium RDases. The recombinant tetrachloroethene RDase (PceA_Y51) appeared to be non-selective towards different Cbas. However, the functional production of the 1,2-dichloroethane-dihaloeliminating enzyme (DcaA) of Desulfitobacterium dichloroeliminans was completely prevented in cells producing 5,6-dimethylbenzimidazolyl-Cba, but substantially enhanced in cells that incorporated 5-methoxybenzimidazole into the Cba cofactor. The results of the study indicate the utilization of a range of different Cbas by Desulfitobacterium RDases with selected representatives apparently preferring distinct Cbas.     

Phytolith‐rich biochar: A potential Si fertilizer in desilicated soils

Silicon (Si) is beneficial to plants since it increases photosynthetic efficiency, and alleviates biotic and abiotic stresses. In the most highly weathered and desilicated soils, plant phytoliths make up the reservoir of bioavailable Si. The regular removal of crop residues, however, substantially decreases this pool. Si supply may therefore be required to sustain continuous cropping. Available Si fertilizers are costly and usually poor in soluble Si. Biochar produced from the pyrolysis of phytolith‐rich biomass is thus a promising alternative Si source for plants. Taking into account the challenges of increasing food demand and environmental concerns, we evaluate the global potential of biochar produced from major crop residues and manures in terms of phytogenic Si (PhSi) supply. Crop residues contribute to 80% of the global production of biomass dry matter (8,201 Tg/year) of which 3,137 Tg/year are potentially available after pyrolysis, giving a potential application rate of 1.7 T ha^?1 year^?1 for highly weathered soils in the tropics. The potential PhSi supply from crop biochar amounts to 102 Tg Si/year. On its own, rice straws produce 57.7 Tg PhSi/year, accounting for 56.6% of the potential annual PhSi production. The Si release from crop biochar depends on inter altere feedstock type, pyrolysis temperature, soil pH, and buffer capacity. Furthermore, the amplitude of plant Si uptake and mineralomass depends on plant species, soil properties, and processes. These factors interact and can exert a decisive influence on the effectiveness of phytolithic biochar in releasing Si into highly weathered soils. We conclude that the use of phytolithic biochar as a Si fertilizer offers undeniable potential to mitigate desilication and to enhance Si ecological services due to soil weathering and biomass removal. This potential must be explored, as well as the conditions for using biochar in the field.     

Fractionation of three different lignins by thermal separation techniques—A comparative study

Separation of the heterogeneous lignin macromolecule in fractions with increased homogeneity, as well as different structural (molar mass) and functional (hydroxy groups, ‐OH) features is important in terms of its use as a chemical building block. For this purpose, three thermal separation techniques were investigated and compared: solvent extraction, successive precipitation and ultrafiltration. One important issue in this context is the utilization of organic solvents with low boiling points to ensure a simple and efficient recovery. In addition to a softwood Kraft lignin (Indulin AT) as reference lignin, two sulfur‐free Organosolv lignins from short rotation coppice (“poplar with bark”) and from the energy grass Miscanthus × gigantheus were investigated. The lignins were separated into low, medium and high molecular weight fractions. Due to the different initial structural features and the associated varying solubility properties in such lignins, different organic solvents were needed for dissolution and precipitation of the individual lignin fractions. The polarity of the used solvent is one key factor regarding the yield of the soluble fraction and the success of molecular sorting into low, medium, and high molecular weight. Further structural features, for example the aliphatic OH‐group content increased with rising molecular weight of poplar, miscanthus, and Kraft lignin from minimum 0.72, 0.3, and 1.6 mmol/g to maximum 2.4, 1.6, and 2.8 mmol/g, respectively. The number of phenolic OH‐groups decreased from maximum 3.8, 4.3, and 4.2 to minimum 1.4, 2.7, and 2.9, respectively. The presented work illustrate options regarding the molecular sorting of several lignin types with three thermal techniques into fractions differing in key properties (yield, molecular weight, polydispersity, functional groups) for material applications.     

Natural climate solutions versus bioenergy: Can carbon benefits of natural succession compete with bioenergy from short rotation coppice?

Short rotation plantations are often considered as holding vast potentials for future global bioenergy supply. In contrast to raising biomass harvests in forests, purpose‐grown biomass does not interfere with forest carbon (C) stocks. Provided that agricultural land can be diverted from food and feed production without impairing food security, energy plantations on current agricultural land appear as a beneficial option in terms of renewable, climate‐friendly energy supply. However, instead of supporting energy plantations, land could also be devoted to natural succession. It then acts as a long‐term C sink which also results in C benefits. We here compare the sink strength of natural succession on arable land with the C saving effects of bioenergy from plantations. Using geographically explicit data on global cropland distribution among climate and ecological zones, regionally specific C accumulation rates are calculated with IPCC default methods and values. C savings from bioenergy are given for a range of displacement factors (DFs), acknowledging the varying efficiency of bioenergy routes and technologies in fossil fuel displacement. A uniform spatial pattern is assumed for succession and bioenergy plantations, and the considered timeframes range from 20 to 100 years. For many parameter settings—in particular, longer timeframes and high DFs—bioenergy yields higher cumulative C savings than natural succession. Still, if woody biomass displaces liquid transport fuels or natural gas‐based electricity generation, natural succession is competitive or even superior for timeframes of 20–50 years. This finding has strong implications with climate and environmental policies: Freeing land for natural succession is a worthwhile low‐cost natural climate solution that has many co‐benefits for biodiversity and other ecosystem services. A considerable risk, however, is C stock losses (i.e., emissions) due to disturbances or land conversion at a later time.     

Structural and functional responses of invertebrate communities to climate change and flow regulation in alpine catchments

Understanding and predicting how biological communities respond to climate change is critical for assessing biodiversity vulnerability and guiding conservation efforts. Glacier‐ and snow‐fed rivers are one of the most sensitive ecosystems to climate change, and can provide early warning of wider‐scale changes. These rivers are frequently used for hydropower production but there is minimal understanding of how biological communities are influenced by climate change in a context of flow regulation. This study sheds light on this issue by disentangling structural (water temperature preference, taxonomic composition, alpha, beta and gamma diversities) and functional (functional traits, diversity, richness, evenness, dispersion and redundancy) effects of climate change in interaction with flow regulation in the Alps. For this, we compared environmental and aquatic invertebrate data collected in the 1970s and 2010s in regulated and unregulated alpine catchments. We hypothesized a replacement of cold‐adapted species by warming‐tolerant ones, high temporal and spatial turnover in taxa and trait composition, along with reduced taxonomic and functional diversities in consequence of climate change. We expected communities in regulated rivers to respond more drastically due to additive or synergistic effects between flow regulation and climate change. We found divergent structural but convergent functional responses between free‐flowing and regulated catchments. Although cold‐adapted taxa decreased in both of them, greater colonization and spread of thermophilic species was found in the free‐flowing one, resulting in higher spatial and temporal turnover. Since the 1970s, taxonomic diversity increased in the free flowing but decreased in the regulated catchment due to biotic homogenization. Colonization by taxa with new functional strategies (i.e. multivoltine taxa with small body size, resistance forms, aerial dispersion and reproduction by clutches) increased functional diversity but decreased functional redundancy through time. These functional changes could jeopardize the ability of aquatic communities facing intensification of ongoing climate change or new anthropogenic disturbances.     

Evidence for a role of protein phosphorylation in the maintenance of the cnidarian–algal symbiosis

The endosymbiotic relationship between cnidarians and photosynthetic dinoflagellate algae provides the foundation of coral reef ecosystems. This essential interaction is globally threatened by anthropogenic disturbance. As such, it is important to understand the molecular mechanisms underpinning the cnidarian–algal association. Here we investigated phosphorylation‐mediated protein signalling as a mechanism of regulation of the cnidarian–algal interaction, and we report on the generation of the first phosphoproteome for the coral model system Aiptasia. Mass spectrometry‐based phosphoproteomics using data‐independent acquisition allowed consistent quantification of over 3,000 phosphopeptides totalling more than 1,600 phosphoproteins across aposymbiotic (symbiont‐free) and symbiotic anemones. Comparison of the symbiotic states showed distinct phosphoproteomic profiles attributable to the differential phosphorylation of 539 proteins that cover a broad range of functions, from receptors to structural and signal transduction proteins. A subsequent pathway enrichment analysis identified the processes of “protein digestion and absorption,” “carbohydrate metabolism,” and “protein folding, sorting and degradation,” and highlighted differential phosphorylation of the “phospholipase D signalling pathway” and “protein processing in the endoplasmic reticulum.” Targeted phosphorylation of the phospholipase D signalling pathway suggests control of glutamate vesicle trafficking across symbiotic compartments, and phosphorylation of the endoplasmic reticulum machinery suggests recycling of symbiosome‐associated proteins. Our study shows for the first time that changes in the phosphorylation status of proteins between aposymbiotic and symbiotic Aiptasia anemones may play a role in the regulation of the cnidarian–algal symbiosis. This is the first phosphoproteomic study of a cnidarian–algal symbiotic association as well as the first application of quantification by data‐independent acquisition in the coral field.     

Tryptamine derivatives disarm colistin resistance in polymyxin-resistant gram-negative bacteria

The last three decades have seen a dwindling number of novel antibiotic classes approved for clinical use and a concurrent increase in levels of antibiotic resistance, necessitating alternative methods to combat the rise of multi-drug resistant bacteria. A promising strategy employs antibiotic adjuvants, non-toxic molecules that disarm antibiotic resistance. When co-dosed with antibiotics, these compounds restore antibiotic efficacy in drug-resistant strains. Herein we identify derivatives of tryptamine, a ubiquitous biochemical scaffold containing an indole ring system, capable of disarming colistin resistance in the Gram-negative bacterial pathogens Acinetobacter baumannii, Klebsiella pneumoniae, and Escherichia coli while having no inherent bacterial toxicity. Resistance was overcome in strains carrying endogenous chromosomally-encoded colistin resistance machinery, as well as resistance conferred by the mobile colistin resistance-1 (mcr-1) plasmid-borne gene. These compounds restore a colistin minimum inhibitory concentration (MIC) below the Clinical & Laboratory Sciences Institute (CLSI) breakpoint in all resistant strains.