Microbial functionality as affected by experimental warming of a temperate mountain forest soil—A metaproteomics survey

Soil microbes play an important role in terrestrial carbon (C) cycling, but their functional response to global warming remains yet unclear. Soil metaproteomics has the potential to contribute to a better understanding of warming effects on soil microbes as proteins specifically represent active microbes and their physiological functioning. To quantify warming effects on microbial proteins and their distribution among different functional and phylogenetic groups, we sampled forest soil that had been artificially warmed (+4 °C) during seven consecutive growing seasons and analyzed its metaproteomic fingerprint and linked to soil respiration as a fundamental ecosystem service. Bacterial protein abundances largely exceeded fungal abundances at the study site but protein abundances showed only subtle differences among control and warmed soil at the phylum and class level, i.e. a temperature-induced decrease in Firmicutes, an increase in Agaricomycetes and Actinobacteria, and a decrease in the Asco/Basidiomycota ratio. Community function in warmed soil showed a clear trend towards increased proteins involved in microbial energy production and conversion, related to the increased CO2 efflux from warmed soil as a result of stress environmental conditions. The differences in community function could be related to specific phyla using metaproteomics, indicating that microbial adaptation to long-term soil warming mainly changed microbial functions, which is related to enhanced soil respiration. The response of soil respiration to warming (+35% soil CO2 efflux during sampling) has not changed over time. Accordingly, potential long-term microbial adaptations to soil warming were too subtle to affect soil respiration rates or, were overlaid by other co-varying factors (e.g. substrate availability)

Amplitude and frequency of wetting and drying cycles drive N2_{2} and N2_{2}O emissions from a subtropical pasture

This study investigated the effects of irrigation frequency on N$_{2}$ and N$_{2}$O emissions from an intensively managed pasture in the subtropics. Irrigation volumes were estimated to replace evapotranspiration and were applied either once (low frequency) or split into four applications (high frequency). To test for legacy effects, a large rainfall event was simulated at the end of the experiment. Over 15 days, 7.9 ± 2.7 kg N$_{2}$ + N$_{2}$O-N ha$^{-1}$ was emitted on average regardless of irrigation frequency, with N$_{2}$O accounting for 25% of overall N$_{2}$ + N$_{2}$O. Repeated, small amounts of irrigation produced an equal amount of N$_{2}$ + N$_{2}$O losses as a single, large irrigation event. The increase in N$_{2}$O emissions after the large rainfall event was smaller in the high-frequency treatment, shifting the N$_{2}$O/(N$_{2}$O + N$_{2}$) ratio towards N$_{2}$, indicating a treatment legacy effect. Cumulative losses of N$_{2}$O and N$_{2}$ did not differ between treatments, but higher CO$_{2}$ emissions were observed in the high-frequency treatment. Our results suggest that the increase in microbial activity and related O$_{2}$ consumption in response to small and repeated wetting events can offset the effects of increased soil gas diffusivity on denitrification, explaining the lack of treatment effect on cumulative N$_{2}$O and N$_{2}$ emissions and the abundance of N cycling marker genes. The observed legacy effect may be linked to increased mineralisation and subsequent increased dissolved organic carbon availability, suggesting that increased irrigation frequency can reduce the environmental impact (N$_{2}$O), but not overall magnitude of N$_{2}$O and N$_{2}$ emissions from intensively managed pastures

Quicklime application instantly increases soil aggregate stability

Agricultural intensification, especially enhanced mechanisation of soil management, can lead to the deterioration of soil structure and to compaction. A possible amelioration strategy is the application of (structural) lime. In this study, we tested the effect of two different liming materials, ie limestone (CaCO3) and quicklime (CaO), on soil aggregate stability in a 3-month greenhouse pot experiment with three agricultural soils. The liming materials were applied in the form of pulverised additives at a rate of 2 000 kg ha1. Our results show a significant and instantaneous increase of stable aggregates after quicklime application whereas no effects were observed for limestone. Quicklime application seems to improve aggregate stability more efficiently in soils with high clay content and cation exchange capacity. In conclusion, quicklime application may be a feasible strategy for rapid improvement of aggregate stability of fine textured agricultural soils.(VLID)224292

Effect of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on N-turnover, the N2_{2}O reductase-gene nosZ and N2_{2}O:N2_{2} partitioning from agricultural soils

Nitrification inhibitors (NIs) have been shown to reduce emissions of the greenhouse gas nitrous oxide (N$_{2}$O) from agricultural soils. However, their N$_{2}$O reduction efficacy varies widely across different agro-ecosystems, and underlying mechanisms remain poorly understood. To investigate effects of the NI 3,4-dimethylpyrazole-phosphate (DMPP) on N-turnover from a pasture and a horticultural soil, we combined the quantification of N$_{2}$ and N$_{2}$O emissions with $^{15}$N tracing analysis and the quantification of the N$_{2}$O-reductase gene (nosZ) in a soil microcosm study. Nitrogen fertilization suppressed nosZ abundance in both soils, showing that high nitrate availability and the preferential reduction of nitrate over N$_{2}$O is responsible for large pulses of N$_{2}$O after the fertilization of agricultural soils. DMPP attenuated this effect only in the horticultural soil, reducing nitrification while increasing nosZ abundance. DMPP reduced N$_{2}$O emissions from the horticultural soil by >50% but did not affect overall N$_{2}$ + N$_{2}$O losses, demonstrating the shift in the N$_{2}$O:N$_{2}$ ratio towards N$_{2}$ as a key mechanism of N$_{2}$O mitigation by NIs. Under non-limiting NO$_{3}$$^{-}$ availability, the efficacy of NIs to mitigate N$_{2}$O emissions therefore depends on their ability to reduce the suppression of the N$_{2}$O reductase by high NO$_{3}$$^{-}$ concentrations in the soil, enabling complete denitrification to N$_{2}$

Shifts in microbial stoichiometry upon nutrient addition do not capture growth-limiting nutrients for soil microorganisms in two subtropical soils

Microbial stoichiometry has become a key aspect in ecological research as shifts in microbial C:N, C:P and N:P ratios upon nutrient addition are presumed to give insight into relative nutrient limitations for soil microorganisms–with far-reaching implications for biogeochemical processes. However, this expectation has never been tested against direct methods of microbial growth responses to nutrient addition. We therefore manipulated a subtropical grassland and forest soil with multifactorial C-, N- and P-additions during 30 days to induce changes in limiting resources and evaluated the resulting soil microbial growth rates, microbial biomass stoichiometry, potential enzyme activities and microbial community composition. Our results show that microbial stoichiometric shifts upon nutrient addition ambiguously predict growth-limiting nutrients for soil microbes. For example, P- and NP-addition to the grassland soil significantly shifted the microbial N:P ratio, which suggests increased N- relative to P-limitation. Microbial growth responses however indicated that soil microbes remained C limited. The same applies for the forest soil, where P-, CN-, NP- and CNP-additions shifted the microbial N:P ratio, yet microbial growth remained C limited. This indicates that microorganisms can immobilize N and P for storage when C is the main limiting nutrient, and that intracellular storage of N and P is responsible for the observed shifts in microbial stoichiometry. Moreover, our data imply that shifts in microbial C:N ratios do not necessarily indicate shifts in microbial community composition and suggest that soil microorganisms–when subject to resource pulses–are stoichiometrically quite plastic

Lachgas und N2-Emissionen intensiv bewirtschafteter Weiden in den australischen Subtropen (Nitrous Oxide and N2 emissions from intensiveliy managed pastures in the Australian Subtropics in response to wetting and drying cycles)

Rainfall and irrigation cause denitrification losses in the form of nitrous oxide (N2O) and dinitrogen (N2) emissions from pasture soils. Nitrous oxide is a potent greenhouse gas, while total N2O and N2 emissions represent a loss of available nitrogen (N) from the soil. In situ measurements of both N2O and N2 are rare, despite their importance to N budgets and the greenhouse gas balance of agroecosystems. This paper presents our research on N2O and N2 emissions from dairy pastures in the Australian subtropics. A series of field studies examined factors determining the temporal and spatial distribution and magnitude of denitrification rates. Furthermore, measures to reduce denitrification losses were investigated that include fertilisation and irrigation. The data obtained provide the basis for predictions using simulation models that examine the long-term effects of agricultural practices on dairy pasture

Does Soil Contribute to the Human Gut Microbiome?

Soil and the human gut contain approximately the same number of active microorganisms, while human gut microbiome diversity is only 10% that of soil biodiversity and has decreased dramatically with the modern lifestyle. We tracked relationships between the soil microbiome and the human intestinal microbiome. We propose a novel environmental microbiome hypothesis, which implies that a close linkage between the soil microbiome and the human intestinal microbiome has evolved during evolution and is still developing. From hunter-gatherers to an urbanized society, the human gut has lost alpha diversity. Interestingly, beta diversity has increased, meaning that people in urban areas have more differentiated individual microbiomes. On top of little contact with soil and feces, hygienic measures, antibiotics and a low fiber diet of processed food have led to a loss of beneficial microbes. At the same time, loss of soil biodiversity is observed in many rural areas. The increasing use of agrochemicals, low plant biodiversity and rigorous soil management practices have a negative effect on the biodiversity of crop epiphytes and endophytes. These developments concur with an increase in lifestyle diseases related to the human intestinal microbiome. We point out the interference with the microbial cycle of urban human environments versus pre-industrial rural environments. In order to correct these interferences, it may be useful to adopt a different perspective and to consider the human intestinal microbiome as well as the soil/root microbiome as ‘superorganisms’ which, by close contact, replenish each other with inoculants, genes and growth-sustaining molecules

Response of Microbial Communities and Their Metabolic Functions to Drying–Rewetting Stress in a Temperate Forest Soil

Global climate change is predicted to alter drought–precipitation patterns, which will likely affect soil microbial communities and their functions, ultimately shifting microbially-mediated biogeochemical cycles. The present study aims to investigate the simultaneous variation of microbial community compositions and functions in response to drought and following rewetting events, using a soil metaproteomics approach. For this, an established field experiment located in an Austrian forest with two levels (moderate and severe stress) of precipitation manipulation was evaluated. The results showed that fungi were more strongly influenced by drying and rewetting (DRW) than bacteria, and that there was a drastic shift in the fungal community towards a more Ascomycota-dominated community. In terms of functional responses, a larger number of proteins and a higher functional diversity were observed in both moderate and severe DRW treatments compared to the control. Furthermore, in both DRW treatments a rise in proteins assigned to “translation, ribosomal structure, and biogenesis„ and “protein synthesis„ suggests a boost in microbial cell growth after rewetting. We also found that the changes within intracellular functions were associated to specific phyla, indicating that responses of microbial communities to DRW primarily shifted microbial functions. Microbial communities seem to respond to different levels of DRW stress by changing their functional potential, which may feed back to biogeochemical cycles