Land-use influences phosphatase gene microdiversity in soils

Phosphorus cycling exerts significant influence upon soil fertility and productivity - processes largely controlled by microbial activity. We adopted phenotypic and metagenomic approaches to investigate phosphatase genes within soils. Microbial communities in bare fallowed soil showed a marked capacity to utilise phytate for growth compared to arable or grassland soil communities. Bare fallowed soil contained lowest concentrations of orthophosphate. Analysis of metagenomes indicated phoA, phoD and phoX, and histidine acid and cysteine phytase genes were most abundant in grassland soil which contained the greatest amount of NaOH-EDTA extractable orthophosphate. Beta-propeller phytase genes were most abundant in bare fallowed soil. Phylogenetic analysis of metagenome sequences indicated the phenotypic shift observed in the capacity to mineralise phytate in bare fallow soil was accompanied by an increase in phoD, phoX and beta-propeller phytase genes coding for exoenzymes. However, there was a remarkable degree of taxonomic similarity across the soils despite the differences in land-use. Predicted extracellular ecotypes were distributed across a greater range of soil structure than predicted intracellular ecotypes, suggesting that microbial communities subject to the dual stresses of low nutrient availability and reduced access to organic material in bare fallowed soils rely upon the action of exoenzymes

Gradual caldera collapse at Bárdarbunga volcano, Iceland, regulated by lateral magma outflow

Large volcanic eruptions on Earth commonly occur with a collapse of the roof of a crustal magma reservoir, forming a caldera. Only a few such collapses occur per century, and the lack of detailed observations has obscured insight into the mechanical interplay between collapse and eruption.We usemultiparameter geophysical and geochemical data to show that the 110-squarekilometer and 65-meter-deep collapse of Bárdarbunga caldera in 2014-2015 was initiated through withdrawal of magma, and lateral migration through a 48-kilometers-long dike, from a 12-kilometers deep reservoir. Interaction between the pressure exerted by the subsiding reservoir roof and the physical properties of the subsurface flow path explain the gradual, nearexponential decline of both collapse rate and the intensity of the 180-day-long eruption.</p

High harmonic generation driven by few-cycle infrared fields in gases and liquids

High-order harmonic generation (HHG) in noble gases serves as the foundation of short-wavelength ultrafast optics and extensive research over the past 30 years has led to a comprehensive understanding of the involved generation processes. For the majority of theses studies, titaniumdoped sapphire lasers were deployed, emitting in the near infrared region at around 800 nm. Photon energies up to around 150 eV with unprecedented pulse durations down to hundreds of attoseconds were reached. However, the low conversion efficiency of the extremely nonlinear process is impeding a high flux of the short-wavelength radiation while intrinsic limitations in the generation process prevent higher photon energies at these driving field wavelengths. More recently, HHG was extended to well-ordered crystalline solids, both semiconductors and dielectrics, with continuing debate about the involved generation mechanism. A conclusive understanding of such high density targets is of particular interest, since it can potentially overcome the limit of the low conversion efficiency. This work describes the extension of high-order harmonic generation light sources to novel regimes with the aim to lift these restriction. In the scope of this work, three projects were taken forward. To detect and fully characterize the generated short-wavelength radiation, a high-order harmonic generation beamline was set up. A custom built and optimized charge detector system was developed and installed, enabling to determine the absolute photon flux of the harmonic emission. Deploying a short-wavelength infrared (1800 nm) few-cylce pulse with an excellent spatial and temporal beam quality and a high pulse energy of 750 μJ extended the accessible photon energy of the emitted soft X-ray radiation to the water window region (284 to 540 eV) and above. The emitted radiation was furthermore fully characterized, confirming its excellent spatial and temporal quality. Further, high-order harmonic generation in the liquid phase was studied, representing a largely unexplored generation medium. The liquid phase constitutes the missing link between a high density well-ordered solid target and an atomic or molecular gas, thus allowing to gain novel insights into the process of HHG. By scanning a number of laser and target parameters, the underlying mechanisms, including the extent of generation in liquid rather than surrounding gas, were investigated.Open Acces

Gene Signatures of T-Cell Activation Can Serve as Predictors of Functionality for SARS-CoV-2-Specific T-Cell Receptors

The importance of T cells in controlling SARS-CoV-2 infections has been demonstrated widely, but insights into the quality of these responses are still limited due to technical challenges. Indeed, understanding the functionality of the T-cell receptor (TCR) repertoire of a polyclonal antigen-specific population still requires the tedious work of T-cell cloning or TCR re-expression and subsequent characterization. In this work, we show that it is possible to discriminate highly functional and bystander TCRs based on gene signatures of T-cell activation induced by recent peptide stimulation. SARS-CoV-2-specific TCRs previously identified by cytokine release after peptide restimulation and subsequent single-cell RNA sequencing were re-expressed via CRISPR-Cas9-mediated gene editing into a Jurkat-based reporter cell line system suitable for high-throughput screening. We could observe differences in SARS-CoV-2 epitope recognition as well as a wide range of functional avidities. By correlating these in vitro TCR engineered functional data with the transcriptomic profiles of the corresponding TCR-expressing parental T cells, we could validate that gene signatures of recent T-cell activation accurately identify and predict truly SARS-CoV-2-specific TCRs. In summary, this work paves the way for alternative approaches useful for the functional analysis of global antigen-specific TCR repertoires with largely improved throughput

Manufacturing triple-isotopically labeled microbial necromass to track C, N and P cycles in terrestrial ecosystems

The functional relevance of microbial necromass in terrestrial biogeochemical cycles remains one of the unresolved mysteries of element cycling in ecosystems, especially considering the high microbial abundance and turnover in soil. We therefore established a protocol to manufacture multi-isotope (14C, 15N and 33P) labeled microbial necromass to comprehensively track the turnover of microbial necromass elements within element cycles. This protocol encompasses the i) microbial cultivation of Pseudomonas kilonensis ACN4 (Gram-negative) and Bacillus licheniformis DSM13 (Gram-positive) on labeled minimal medium as well as fungal cultivation of Hypsizygus tessulatus on a complex yeast medium, ii) quantification of radio- (14C, 33P) and stable (15N) isotope incorporation as well their cellular pool partitioning, and iii) determination of element and tracer isotope uptake efficiency. We achieved 1 g of bacterial biomass per liter minimum medium within 24 h and 2.9 g l-1 fungal biomass in complex medium within 18 d. This production rate enabled us to produce more than 100 g of necromass within only one half-life time of 33P, including post-harvest processing. Isotope uptake and incorporation for 33P ranged from 10 to 73%, for 15N from 24 to 52%, and for 14C from 12 to 23%. Each of the cultivated species showed individual patterns of tracer element uptake. The nutritional value of the carbon- (C), nitrogen- (N) and phosphorus- (P) labeled microbial necromass was characterized by a water-based, necromass speciesspecific partitioning scheme with subsequent elemental analysis of the pools. We separated Gram-negative, Gram-positive and fungi’s cellular pools to characterize element and tracer partitioning among dissolved versus particulate fractions. That is essential because these properties subsequently affect the respective pool's availability for ecosystem nutrition. Our procedure allows a defined production of microorganism-based necromass, enabling versatile use to determine necromass-related nutrient fluxes in terrestrial ecosystem studies

Direct Observation of Ultrafast Exciton Localization in an Organic Semiconductor with Soft X-ray Transient Absorption Spectroscopy

We report the first demonstration of time-resolved X-ray absorption spectroscopy to track previously undetected photoinduced dynamics of a paradigmatic crystalline conjugated polymer: poly(3-hexylthiophene) (P3HT) commonly used in solar cell devices. The pi to pi* transition, the first step of solar energy conversion, is pumped with a 15 fs optical pulse and the dynamics are probed by an attosecond soft X-ray pulse at the carbon K-edge. We observe direct spectroscopic signatures of the initially hot excitonic state, which is delocalized over multiple polymer chains, undergoing a rapid evolution on a sub 50 fs timescale which can be directly associated with cooling and localization to form the lowest excitonic state on a single polymer chain. This sensitivity of time-resolved X-ray spectroscopy to the primary electron dynamics occurring directly after excitation paves the way for new insights in a wide range of organic optoelectronic materials