A conditional marker gene allowing both positive and negative selection in plants

Selectable markers enable transgenic plants or cells to be identified after transformation. They can be divided into positive and negative markers conferring a selective advantage or disadvantage, respectively. We present a marker gene, dao1, encoding D-amino acid oxidase (DAAO, EC 1.4.3.3) that can be used for either positive or negative selection, depending on the substrate. DAAO catalyzes the oxidative deamination of a range of D-amino acids. Selection is based on differences in the toxicity of different D-amino acids and their metabolites to plants. Thus, D-alanine and D-serine are toxic to plants, but are metabolized by DAAO into nontoxic products, whereas D-isoleucine and D-valine have low toxicity, but are metabolized by DAAO into the toxic keto acids 3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate, respectively. Hence, both positive and negative selection is possible with the same marker gene. The marker has been successfully established in Arabidopsis thaliana, and proven to be versatile, rapidly yielding unambiguous results, and allowing selection immediately after germination

Decadal nitrogen addition alters chemical composition of soil organic matter in a boreal forest

Boreal forests store approximately 470 Pg of carbon (C) in the soil, and rates of soil C accumulation are significantly enhanced by long-term nitrogen (N) enrichment. Dissecting the compositional profile of soils could help better understand the potential mechanisms driving changes in C cycling under enriched N conditions.We examined the impacts of long-term N addition on the chemical composition of soil organic matter (SOM) in a mature boreal forest. Two large experimental plots (15 ha each) were established: a control and a fertilised plot. The latter received NH4NO3 fertilizer at an average rate of 75 kg N ha(-1) year for 12 years. While the centre of this plot received the prescribed amounts of fertilizer, the year-to-year variation in distribution of fertilizer around the designated edges of the plot created a gradient in N-loading. Along this gradient, a compositional shift in SOM in the organic horizon was assessed using two methods: pyrolysis-gas chromatography/mass spectrometry (GC/MS) and solid-state C-13 nuclear magnetic resonance spectroscopy (C-13 NMR).Both of these methods revealed that the chemical composition of SOM changed with increasing N loading, with an increased fraction of lignin derivatives (i.e., aromatic, methoxy/N-alkyl C) relative to that of carbohydrate (i.e., 0-alkyl C), accompanied by increased soil C mass (kg m(-2)) at the fertilised plot. Also, the relative abundance of N compounds in the pyrolysis products increased with the N loading, mainly due to increased methyl N-acetyl-alpha(D)-glucosaminide in the F/H horizon, plausibly of microbial origin. Microbial N processing likely contributed to soil accumulation of fertilizer-derived N.Our results corroborate the hypothesis that addition of inorganic N suppresses enzymatic white-rot decomposition relative to non-enzymatic brown-rot oxidation. Taken together, our study suggests that N enrichment leads to a selective accumulation of lignin-derived compounds and points to a key role of such compounds for N-induced SOM accumulation

The carbon bonus of organic nitrogen enhances nitrogen use efficiency of plants

The importance of organic nitrogen (N) for plant nutrition and productivity is increasingly being recognized. Here we show that it is not only the availability in the soil that matters, but also the effects on plant growth. The chemical form of N taken up, whether inorganic (such as nitrate) or organic (such as amino acids), may significantly influence plant shoot and root growth, and nitrogen use efficiency (NUE). We analysed these effects by synthesizing results from multiple laboratory experiments on small seedlings (Arabidopsis, poplar, pine and spruce) based on a tractable plant growth model. A key point is that the carbon cost of assimilating organic N into proteins is lower than that of inorganic N, mainly because of its carbon content. This carbon bonus makes it more beneficial for plants to take up organic than inorganic N, even when its availability to the roots is much lower - up to 70% lower for Arabidopsis seedlings. At equal growth rate, root:shoot ratio was up to three times higher and nitrogen productivity up to 20% higher for organic than inorganic N, which both are factors that may contribute to higher NUE in crop production

Using microdialysis with a deuterium oxide tracer to estimate water exchange, water content and active surface area of the probe

Microdialysis is a useful tool for measuring in situ fluxes of soil compounds with minimal disturbance of soil structure and function. Fluxes of sampled compounds are commonly calculated per unit of membrane surface area, assuming that the entire membrane surface is capable of exchange - which is unlikely given varying soil moisture and the occlusion of membrane pores by the soil solid phase. We present a method to quantify the degree of connectivity of the microdialysis probe membrane to the surrounding soil by means of water exchange between a microdialysis perfusate and soil solution using deuterium (2H2O; equilibrated to DHO) as an internal standard. We applied the method to a range of probe membrane surface areas and soil moisture conditions to generate empirical models that estimate membrane surface area active in exchange. Our results suggest that even in a saturated sandy soil, active membrane surface areas reach only 40.3% of the probe surface area, perhaps due to occlusion by soil particles. However, when accounting for volumetric water content of the soil, active surface areas approached 80-90% of the area likely in contact with water, indicating that sampling efficiency of waterfilled pores may still be high, particularly at slow flow rates. Furthermore, our method enables assessment of local soil water content around the probe. Models estimating soil water content were applied to field measurements of DHO exchange in three soil horizons (Organic, B1, B2) at two boreal sites, and in situ estimates were similar to those from conventional soil moisture methods when models were calibrated with the same soil type. We present DHO exchange as a powerful method for improving microdialysis flux interpretations in future studies, and for exploring small-scale water variability in relatively undisturbed soils

Components explain, but do eddy fluxes constrain? Carbon budget of a nitrogen-fertilized boreal Scots pine forest

Nitrogen (N) fertilization increases biomass and soil organic carbon (SOC) accumulation in boreal pine forests, but the underlying mechanisms remain uncertain. At two Scots pine sites, one undergoing annual N fertilization and the other a reference, we sought to explain these responses.We measured component fluxes, including biomass production, SOC accumulation, and respiration, and summed them into carbon budgets. We compared the resulting summations to ecosystem fluxes measured by eddy covariance.N fertilization increased most component fluxes (P −2 yr−1. Stemwood production increases were ascribed to this partitioning shift, gross primary production (GPP), and carbon-use efficiency, in that order. The methods agreed in their estimates of GPP in both stands (P > 0.05), but the components detected an increase in net ecosystem production (NEP) (190 (54) g C m−2 yr−1; P −2 yr−1; ns).The pairing of plots, the simplicity of the sites, and the strength of response provide a compelling description of N effects on the C budget. However, the disagreement between methods calls for further paired tests of N fertilization effects in simple forest ecosystems

Biohybrid plants with electronic roots via in vivo polymerization of conjugated oligomers

Plant processes, ranging from photosynthesis through production of biomaterials to environmental sensing and adaptation, can be used in technology via integration of functional materials and devices. Previously, plants with integrated organic electronic devices and circuits distributed in their vascular tissue and organs have been demonstrated. To circumvent biological barriers, and thereby access the internal tissue, plant cuttings were used, which resulted in biohybrids with limited lifetime and use. Here, we report intact plants with electronic functionality that continue to grow and develop enabling plant-biohybrid systems that fully maintain their biological processes. The biocatalytic machinery of the plant cell wall was leveraged to seamlessly integrate conductors with mixed ionic-electronic conductivity along the root system of the plants. Cell wall peroxidases catalyzed ETE-S polymerization while the plant tissue served as the template, organizing the polymer in a favorable manner. The conductivity of the resulting p(ETE-S) roots reached the order of 10 S cm(-1) and remained stable over the course of 4 weeks while the roots continued to grow. The p(ETE-S) roots were used to build supercapacitors that outperform previous plant-biohybrid charge storage demonstrations. Plants were not affected by the electronic functionalization but adapted to this new hybrid state by developing a more complex root system. Biohybrid plants with electronic roots pave the way for autonomous systems with potential applications in energy, sensing and robotics