Biotic and abiotic control of microbial community structure and activity in forest soils

Microorganisms are the key drivers of most processes in soil. Therefore, factors regulating microbial composition, functions and activities are hot topics in soil science. Focusing on forest ecosystems, this PhD aimed to evaluate: i) abiotic (temperature and precipitation) and biotic (trees species identity) factors regulating the composition of microbial communities in forest soils, ii) the effects of forest biodiversity on microbial decomposition of organic polymeric compounds of plant litter and iii) the effects of intrinsic properties of common low molecular weight organic substances (LMWOS) on their microbial uptake and subsequent metabolization by soil microorganisms. It was found that abiotic factors affect soil microbial community structure in forests indirectly, mainly via modification of environmental conditions (soil pH, carbon (C) and nitrogen (N) contents) and plant productivity, which was studied for the old deciduous ecosystems along a climosequence gradient of Mt. Kilimanjaro. Effects of biotic factors on microbial communities was checked for the young (10-year-old) monoculture forest in comparison with forests from mixed species with contrasting functional traits (i.e. early primary (birch and alder) vs. late successional species (beech and oak), and N-fixing (alder) vs. non-N- fixing (birch, beech and oak)) to reveal direct impact of litter quality changes, before strong modification of edaphic factors occurs. Afforestation had stronger effects on the development of fungal (increased by 50-200% based on the biomarker analysis) than of bacterial communities (increased by 20-120%). These effects were proved for all forests, but were more pronounced under the monocultures compared to mixtures. Consequently, species identity has stronger effects than diversity on the formation of microbial community structure in soil. Enzyme systems, responsible for decomposition of plant litter, reacted differently to afforestation with species having contrasting functional traits, even for the enzymes responsible for one element (C or N). The maximum activities of β-N-acetylglucosaminidase, β-xylosidase and acid phosphatase were found for the sites, where early primary species (birch) developed simultaneously with late successional species (beech and oak), showing synergistic effects. In contrast, development of beech in monoculture strongly suppressed enzyme activities. The effects of forest biodiversity on element dynamics in soil were proven by N functional genes abundance and N cycling rates (gross and net nitrification and ammonification). N functional genes abundance is less sensitive parameter to reveal significant effects of forest biodiversity on N cycling at the early stage of afforestation compared to direct measurement of N cycling rates, and both parameters Thesis summary should be accounted. Forest composition affects microbial utilization of common LMWOS, but there is a knowledge gap regarding i) an appropriate review on the composition, content of fate of sugars in the soils, which are the main C and energy source of microorganisms and ii) effects of intrinsic properties of LMWOS (C oxidation state, molecular weight, number of C atoms) on their utilization by microorganisms. For the first question, a literature review has revealed that sugars are subjected to intensive recycling in soil: 80% of all sugars are recycled microbial compounds and only 20% are originated from plant biomass. For the second question, substances with C oxidation states varying from '0' (glucose, fructose and alanine) to '+0.5' (succinic acid), '+1' (glycine and malic acid) and '+2' (formic acid) were studied. The C oxidation state of LMWOS correlated significantly with their half-life (T½) in soil solution, with more oxidized substances (formic acid) being utilized by microorganisms six times faster than less oxidized substances (sugars). In contrast, LMWOS-C oxidation state had no effect on the T½ of C incorporated into microbial biomass due to cell metabolites produced from the initial LMWOS. The portion of mineralized LMWOS increased with their C oxidation state, being 4.5 times higher for formic acid compare to sugars, and corresponded to the decrease of C incorporated into microbial biomass and soil organic matter pools. In conclusion, biotic factors such as tree species should be accounted when studying microbial community composition in forest soils. However, abiotic factors play a secondary role and are strongly mediated by biotic controls. To quantify the role of microbial functions for the decomposition of litter-derived organic compounds biochemical (enzyme activities) and molecular methods (e.g. functional gene abundance), as well as direct measurements of process rates (e.g. decomposition nitrification or ammonification rates), should be performed in combination and related to the molecular properties (e.g. C oxidation state) of the microbially utilized substances

To Be or Not To Be a Molecular Ion: The Role of the Solvent in Photoionization of Arginine.

Application of photoionization mass spectroscopy, a technique capable of assessing protonation states in complex molecules in the gas phase, is challenging for arginine due to its fragility. We report photoionization efficiencies in the valence region of aqueous aerosol particles produced from arginine solutions under various pH and vaporization conditions. By using ab initio calculations, we investigate the stability of different conformers. Our results show that neutral arginine fragments upon ionization in the gas phase but solvation stabilizes the molecular ion, resulting in different photoionization dynamics. We also report the valence-band photoelectron spectra of the aerosol solutions obtained at different pH values

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design