Management versus site effects on the abundance of nitrifiers and denitrifiers in European mountain grasslands

It is well established that the abundances of nitrogen (N) transforming microbes are strongly influenced by land-use intensity in lowland grasslands. However, their responses to management change in less productive and less fertilized mountain grasslands are largely unknown. We studied eight mountain grasslands, positioned along gradients of management intensity in Austria, the UK, and France, which differed in their historical management trajectories. We measured the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as nitrite-reducing bacteria using specific marker genes. We found that management affected the abundance of these microbial groups along each transect, though the specific responses differed between sites, due to different management histories and resulting variations in environmental parameters. In Austria, cessation of management caused an increase in nirK and nirS gene abundances. In the UK, intensification of grassland management led to 10-fold increases in the abundances of AOA and AOB and doubling of nirK gene abundance. In France, ploughing of previously mown grassland caused a 20-fold increase in AOA abundance. Across sites the abundance of AOB was most strongly related to soil NO3−-N availability, and AOA were favored by higher soil pH. Among the nitrite reducers, nirS abundance correlated most strongly with N parameters, such as soil NO3−-N, microbial N, leachate NH4+-N, while the abundance of nirK-denitrifiers was affected by soil total N, organic matter (SOM) and water content. We conclude that alteration of soil environmental conditions is the dominant mechanism by which land management practices influence the abundance of each group of ammonia oxidizers and nitrite reducers

Effects of drought on nitrogen turnover and abundances of ammonia-oxidizers in mountain grassland

Future climate scenarios suggest an increased frequency of summer drought periods in the European Alpine Region. Drought can affect soil nitrogen (N) cycling, by altering N transformation rates, as well as the abundances of ammonia-oxidizing bacteria and archaea. However, the extent to which drought affects N cycling under in situ conditions is still controversial. The goal of this study was to analyse effects of drought on soil N turnover and ammoniaoxidizer abundances in soil without drought history. To this end we conducted rain-exclusion experiments at two differently managed mountain grassland sites, an annually mown and occasionally fertilized meadow and an abandoned grassland. Soils were sampled before, during and after drought and were analysed for potential gross rates of N mineralization, microbial uptake of inorganic N, nitrification, and the abundances of bacterial and archaeal ammonia-oxidizers based on gene copy numbers of the amoA gene (AOB and AOA, respectively). Drought induced different responses at the two studied sites. At the managed meadow drought increased NH+/4 immobilization rates and NH+/4 concentrations in the soil water solution, but led to a reduction of AOA abundance compared to controls. At the abandoned site gross nitrification and NO-/3 immobilization rates decreased during drought, while AOB and AOA abundances remained stable. Rewetting had only minor, short-term effects on the parameters that had been affected by drought. Seven weeks after the end of drought no differences to control plots could be detected. Thus, our findings demonstrated that in mountain grasslands drought had distinct transient effects on soil nitrogen cycling and ammonia-oxidizers, which could have been related to a niche differentiation of AOB and AOA with increasing NH+/4 levels. However, the effect strength of drought was modulated by grassland management

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. Acknowledgements We would like to thank Dr Robert Griffith/CEH for providing DNA from soil samples and Dr Anthony Travis for his help with BioLinux. Sequencing was performed in NERC platform in Liverpool. CG-R was funded by a NERC fellowship NE/J019151/1. CQ was funded by a MRC fellowship (MR/M50161X/1) as part of the cloud infrastructure for microbial genomics consortium (MR/L015080/1).Peer reviewedPublisher PD

Quantitative assessment of hydrolase production and persistence in soil

The aim of this work was to calculate indices of hydrolase production (Pr) and persistence (Pe) through simple arithmetical calculations. Changes in acid and alkaline phosphomonoesterase, phosphodiesterase, urease, protease, and \u3b2-glucosidase activities were monitored under controlled conditions in seven soils with a wide range of properties, in which microbial growth was stimulated by adding glucose and nitrogen. Glucose mineralization was monitored by CO2-C evolution, and microbial growth was quantified by determining the soil adenosine triphosphate (ATP) content. Hydrolase Pr and Pe indices were numerically quantified by the following relationships: Pr = H / t H and Pe = (r / H)\u394t, respectively, where H indicates the peak value of each measured hydrolase activity, t H is the time of the peak value, r indicates the residual activity value, and \u394t is the time interval t r - t H, where t r is the time of the residual activity value. Addition of glucose and N-stimulated soil respiration increased ATP content and stimulated the production of the measured hydrolase activities in all soils; the measured variable reached a maximum value and then decreased, returning to the value of the control soil. Apart from \u3b2-glucosidase activity, whose activity was not stimulated by glucose and N addition, the other measured hydrolase activities showed a trend that allowed us to calculate the Pr and Pe indices using the above-mentioned equations. Acid phosphomonoesterase and protease Pr values were significantly higher in soils under forest or set aside management; the alkaline phosphomonoesterase and phosphodiesterase Pr values were generally higher in the neutral and alkaline soils, and the urease Pr values showed no obvious relationships with soil pH or management. Concerning the persistence of enzyme activities, Pe values of the acid phosphomonoesterase activity were significantly higher in the acidic soils, and those of urease activity were higher in acidic soils and the Bordeaux neutral soil. No relationships were observed between Pe values of alkaline phosphomonoesterase, phosphodiesterase, or protease activities and soil pH or management. The different responses of hydrolases were discussed in relation to soil properties, microbial growth, and regulation at the enzyme molecular level

Ammonia-oxidation as an engine to generate nitrous oxide in an intensively managed calcareous Fluvo-aquic soil

We combine field observations, microcosm, stoichiometry, and molecular and stable isotope techniques to quantify N(2)O generation processes in an intensively managed low carbon calcareous fluvo-aquic soil. All the evidence points to ammonia oxidation and linked nitrifier denitrification (ND) being the major processes generating N(2)O. When NH(4)(+)-based fertilizers are applied the soil will produce high N(2)O peaks which are inhibited almost completely by adding nitrification inhibitors. During ammonia oxidation with high NH(4)(+) concentrations (>80 mg N kg(−1)) the soil matrix will actively consume oxygen and accumulate high concentrations of NO(2)(−), leading to suboxic conditions inducing ND. Calculated N(2)O isotopomer data show that nitrification and ND accounted for 35–53% and 44–58% of total N(2)O emissions, respectively. We propose that slowing down nitrification and avoiding high ammonium concentrations in the soil matrix are important measures to reduce N(2)O emissions per unit of NH(4)(+)-based N input from this type of intensively managed soil globally

Biological soil crusts increase the resistance of soil nitrogen dynamics to changes in temperatures in a semi-arid ecosystem

Aims: Biological soil crusts (BSCs), composed of mosses, lichens, liverworts and cyanobacteria, are a key component of arid and semi-arid ecosystems worldwide, and play key roles modulating several aspects of the nitrogen (N) cycle, such as N fixation and mineralization. While the performance of its constituent organisms largely depends on moisture and rainfall conditions, the influence of these environmental factors on N transformations under BSC soils has not been evaluated before. Methods: The study was done using soils collected from areas devoid of vascular plants with and without lichen-dominated BSCs from a semi-arid Stipa tenacissima grassland. Soil samples were incubated under different temperature (T) and soil water content (SWC) conditions, and changes in microbial biomass-N, dissolved organic nitrogen (DON), amino acids, ammonium, nitrate and both inorganic N were monitored. To evaluate how BSCs modulate the resistance of the soil to changes in T and SWC, we estimated the Orwin and Wardle Resistance index. Results: The different variables studied were more affected by changes in T than by variations in SWC at both BSC-dominated and bare ground soils. However, under BSCs, a change in the dominance of N processes from a net nitrification to a net ammonification was observed at the highest SWC, regardless of T. Conclusions: Our results suggest that the N cycle is more resistant to changes in T in BSC-dominated than in bare ground areas. They also indicate that BSCs could play a key role in minimizing the likely impacts of climate change on the dynamics of N in semi-arid environments, given the prevalence and cover of these organisms worldwide