Resistance and resilience of the forest soil microbiome to logging-associated compaction

Soil compaction is a major disturbance associated with logging, but we lack a fundamental understanding of how this affects the soil microbiome. We assessed the structural resistance and resilience of the microbiome using a high-throughput pyrosequencing approach in differently compacted soils at two forest sites and correlated these findings with changes in soil physical properties and functions. Alterations in soil porosity after compaction strongly limited the air and water conductivity. Compaction significantly reduced abundance, increased diversity, and persistently altered the structure of the microbiota. Fungi were less resistant and resilient than bacteria; clayey soils were less resistant and resilient than sandy soils. The strongest effects were observed in soils with unfavorable moisture conditions, where air and water conductivities dropped well below 10% of their initial value. Maximum impact was observed around 6-12 months after compaction, and microbial communities showed resilience in lightly but not in severely compacted soils 4 years post disturbance. Bacteria capable of anaerobic respiration, including sulfate, sulfur, and metal reducers of the Proteobacteria and Firmicutes, were significantly associated with compacted soils. Compaction detrimentally affected ectomycorrhizal species, whereas saprobic and parasitic fungi proportionally increased in compacted soils. Structural shifts in the microbiota were accompanied by significant changes in soil processes, resulting in reduced carbon dioxide, and increased methane and nitrous oxide emissions from compacted soils. This study demonstrates that physical soil disturbance during logging induces profound and long-lasting changes in the soil microbiome and associated soil functions, raising awareness regarding sustainable management of economically driven logging operations.

Soil environmental conditions and microbial build-up mediate the effect of plant diversity on soil nitrifying and denitrifying enzyme activities in temperate grasslands

Random reductions in plant diversity can affect ecosystem functioning, but it is still unclear which components of plant diversity (species number - namely richness, presence of particular plant functional groups, or particular combinations of these) and associated biotic and abiotic drivers explain the observed relationships, particularly for soil processes. We assembled grassland communities including 1 to 16 plant species with a factorial separation of the effects of richness and functional group composition to analyze how plant diversity components influence soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), the abundance of nitrifiers (bacterial and archaeal amoA gene number) and denitrifiers (nirK, nirS and nosZ gene number), and key soil environmental conditions. Plant diversity effects were largely due to differences in functional group composition between communities of identical richness (number of sown species), though richness also had an effect per se. NEA was positively related to the percentage of legumes in terms of sown species number, the additional effect of richness at any given legume percentage being negative. DEA was higher in plots with legumes, decreased with increasing percentage of grasses, and increased with richness. No correlation was observed between DEA and denitrifier abundance. NEA increased with the abundance of ammonia oxidizing bacteria. The effect of richness on NEA was entirely due to the build-up of nitrifying organisms, while legume effect was partly linked to modified ammonium availability and nitrifier abundance. Richness effect on DEA was entirely due to changes in soil moisture, while the effects of legumes and grasses were partly due to modified nitrate availability, which influenced the specific activity of denitrifiers. These results suggest that plant diversity-induced changes in microbial specific activity are important for facultative activities such as denitrification, whereas changes in microbial abundance play a major role for non-facultative activities such as nitrification.

Soil nitrogen dynamics in a river floodplain mosaic

In their natural state, river floodplains are heterogeneous and dynamic ecosystems that may retain and remove large quantities of nitrogen from surface waters. We compared the soil nitrogen dynamics in different types of habitat patches in a restored and a channelized section of a Thur River floodplain (northeast Switzerland). Our objective was to relate the spatiotemporal variability of selected nitrogen pools (ammonium, nitrate, microbial nitrogen), nitrogen transformations (mineralization, nitrification, denitrification), and gaseous nitrogen emission (NO) to soil properties and hydrological processes. Our study showed that soil water content and carbon availability, which depend on sedimentation and inundation dynamics, were the key factors controlling nitrogen pools and processes. High nitrogen turnover rates were measured on gravel bars, characterized by both frequent inundation and high sediment deposition rates, as well as in low-lying alluvial forest patches with a fine-textured, nutrient-rich soil where anaerobic microsites probably facilitated coupled nitrification-denitrification. In contrast, soils of the embankment in the channelized section had comparatively small inorganic nitrogen pools and low transformation rates, particularly those related to nitrate production. Environmental heterogeneity, characteristic of the restored section, favors nitrogen removal by creating sites of high sedimentation and denitrification. Of concern, however, are the locally high NO efflux and the possibility that nitrate could leach from nitrification hotspots.

Analysis of carbon and nitrogen dynamics in riparian soils: model validation and sensitivity to environmental controls

The Riparian Soil Model (RSM) of Brovelli et al. (2012) was applied to study soil nutrient turnover in a revitalized section of the Thur River, North-East Switzerland. In the present work, the model was calibrated on field experimental data, and satisfactorily reproduced soil respiration, organic matter stocks and inorganic nitrogen fluxes. Calibrated rates were in good agreement with the ranges reported in the literature. The main discrepancies between model and observations were for dissolved organic carbon. The sensitivity of the model to environmental factors was also analyzed. Soil temperature was the most influential factor at daily and seasonal scales while effects of soil moisture were weak overall. The ecosystem sensitivity to temperature changes was quantified using the Q10 index. The seasonal behavior observed was related to the influence of other forcing factors and to the different state (density and activity) of the microbial biomass pool during the year. Environmental factors influencing microbial decomposition, such as the C:N ratio and litter input rate, showed intermediate sensitivity. Since these parameters are tightly linked to the vegetation type, the analysis highlighted the effect of the aboveground ecosystem on soil functioning.

Above- and below-ground methane fluxes and methanotrophic activity in a landfill-cover soil

Landfills are a major anthropogenic source of the greenhouse gas methane (CH(4)). However, much of the CH(4) produced during the anaerobic degradation of organic waste is consumed by methanotrophic microorganisms during passage through the landfill-cover soil. On a section of a closed landfill near Liestal, Switzerland, we performed experiments to compare CH(4) fluxes obtained by different methods at or above the cover-soil surface with below-ground fluxes, and to link methanotrophic activity to estimates of CH(4) ingress (loading) from the waste body at selected locations. Fluxes of CH(4) into or out of the cover soil were quantified by eddy-covariance and static flux-chamber measurements. In addition, CH(4) concentrations at the soil surface were monitored using a field-portable FID detector. Near-surface CH(4) fluxes and CH(4) loading were estimated from soil-gas concentration profiles in conjunction with radon measurements, and gas push-pull tests (GPPTs) were performed to quantify rates of microbial CH(4) oxidation. Eddy-covariance measurements yielded by far the largest and probably most representative estimates of overall CH(4) emissions from the test section (daily mean up to ∼91,500μmolm(-2)d(-1)), whereas flux-chamber measurements and CH(4) concentration profiles indicated that at the majority of locations the cover soil was a net sink for atmospheric CH(4) (uptake up to -380μmolm(-2)d(-1)) during the experimental period. Methane concentration profiles also indicated strong variability in CH(4) loading over short distances in the cover soil, while potential methanotrophic activity derived from GPPTs was high (v(max)∼13mmolL(-1)(soil air)h(-1)) at a location with substantial CH(4) loading. Our results provide a basis to assess spatial and temporal variability of CH(4) dynamics in the complex terrain of a landfill-cover soil.

Diversity promotes temporal stability across levels of ecosystem organization in experimental grasslands

The diversity-stability hypothesis states that current losses of biodiversity can impair the ability of an ecosystem to dampen the effect of environmental perturbations on its functioning. Using data from a long-term and comprehensive biodiversity experiment, we quantified the temporal stability of 42 variables characterizing twelve ecological functions in managed grassland plots varying in plant species richness. We demonstrate that diversity increases stability i) across trophic levels (producer, consumer), ii) at both the system (community, ecosystem) and the component levels (population, functional group, phylogenetic clade), and iii) primarily for aboveground rather than belowground processes. Temporal synchronization across studied variables was mostly unaffected with increasing species richness. This study provides the strongest empirical support so far that diversity promotes stability across different ecological functions and levels of ecosystem organization in grasslands.

Competition for light causes plant biodiversity loss after eutrophication

Human activities have increased the availability of nutrients in terrestrial and aquatic ecosystems. In grasslands, this eutrophication causes loss of plant species diversity, but the mechanism of this loss has been difficult to determine. Using experimental grassland plant communities, we found that addition of light to the grassland understory prevented the loss of biodiversity caused by eutrophication. There was no detectable role for competition for soil resources in diversity loss. Thus, competition for light is a major mechanism of plant diversity loss after eutrophication and explains the particular threat of eutrophication to plant diversity. Our conclusions have implications for grassland management and conservation policy and underscore the need to control nutrient enrichment if plant diversity is to be preserved.

Water relations in grassland and desert ecosystems exposed to elevated atmospheric CO2

Atmospheric CO2 enrichment may stimulate plant growth directly through (1) enhanced photosynthesis or indirectly, through (2) reduced plant water consumption and hence slower soil moisture depletion, or the combination of both. Herein we describe gas exchange, plant biomass and species responses of five native or semi-native temperate and Mediterranean grasslands and three semi-arid systems to CO2 enrichment, with an emphasis on water relations. Increasing CO2 led to decreased leaf conductance for water vapor, improved plant water status, altered seasonal evapotranspiration dynamics, and in most cases, periodic increases in soil water content. The extent, timing and duration of these responses varied among ecosystems, species and years. Across the grasslands of the Kansas tallgrass prairie, Colorado shortgrass steppe and Swiss calcareous grassland, increases in aboveground biomass from CO2 enrichment were relatively greater in dry years. In contrast, CO2-induced aboveground biomass increases in the Texas C3/C4 grassland and the New Zealand pasture seemed little or only marginally influenced by yearly variation in soil water, while plant growth in the Mojave Desert was stimulated by CO2 in a relatively wet year. Mediterranean grasslands sometimes failed to respond to CO2-related increased late-season water, whereas semiarid Negev grassland assemblages profited. Vegetative and reproductive responses to CO2 were highly varied among species and ecosystems, and did not generally follow any predictable pattern in regard to functional groups. Results suggest that the indirect effects of CO2 on plant and soil water relations may contribute substantially to experimentally induced CO2-effects, and also reflect local humidity conditions. For landscape scale predictions, this analysis calls for a clear distinction between biomass responses due to direct CO2 effects on photosynthesis and those indirect CO2 effects via soil moisture as documented here.

A link between plant diversity, elevated CO2 and soil nitrate

Interactive effects of reductions in plant species diversity and increases in atmospheric CO₂ were investigated in a long-term study in nutrient-poor calcareous grassland. Throughout the experiment, soil nitrate was persistently increased at low plant species diversity, and CO₂ enrichment reduced soil [NO₃^-] at all levels of plant species diversity. In our study, soil [NO₃^-] was unrelated to root length density, microbial biomass N, community legume contents, and experimental plant communities differed only little in total N pools. However, potential nitrification revealed exactly the same treatment effects as soil [NO₃^-], providing circumstantial evidence that nitrification rates drove the observed changes in [NO₃^-]. One possible explanation for plant diversity effects on nitrification lies in spatial and temporal interspecific differences in plant N uptake, which would more often allow accumulation of NH₄⁺ in part of the soil profile at low diversity than in more species-rich plant communities. Consequently, nitrification rates and soil [NO₃^-] would increase. Elevated CO₂ increased soil water contents, which may have improved NO₃^- diffusion to the root surface thereby reducing soil [NO₃^-]. Higher soil moisture at elevated CO₂ might also reduce nitrification rates due to less aerobic conditions. The accordance of the diversity effect on soil [NO₃^-] with previous experiments suggests that increased soil [NO₃^-] at low species diversity is a fairly general phenomenon, although the mechanisms causing high [NO₃^-] may vary. In contrast, experimental evidence for effects of CO₂ enrichment on soil [NO₃^-] is ambiguous, and the antagonistic interaction of plant species reductions and elevated CO₂ we have observed is thus probably less universal.

Soil moisture effects determine CO2 responses of grassland species

It has been suggested that positive biomass responses of grassland to elevated CO₂ result from moisture savings in the soil as opposed to direct photosynthetic stimulation. In order to test this hypothesis for calcareous grassland we subjected experimental communities consisting of two important graminoid components of such grasslands (Carex flacca and Bromus erectus) on natural substrate to a fully factorial treatment of ambient (360 ppm) and elevated (600 ppm) CO₂ concentration and four irrigation regimes (9 mm, 18 mm, 27 mm and 36 mm week^-1). Biomass stimulation under elevated CO₂ was higher the lower the irrigation rate was. Superimposed on the effects of irrigation on soil moisture, elevated CO₂-induced higher soil water contents in all irrigation treatments via reduced plant water consumption (on average one-third lower stomatal conductance). This led to eight different soil moisture regimes instead of the intended four. When growth parameters were plotted against the effective soil water content rather than irrigation treatment, the "pure" CO₂ effect on total biomass and other traits became much smaller and completely disappeared for biomass per tiller, leaf area per ground area, leaf mass fraction (LMF) and root mass fraction (RMF). We conclude that the CO₂ response observed in this graminoid system consisted of a small primary CO₂ effect and a large secondary, CO₂-induced, soil moisture effect. Thus, it is difficult to use responses to CO₂ from experiments in which CO₂-induced soil moisture savings occur to predict CO₂ effects as long as future soil moisture regimes are not defined. We suggest that direct and indirect (moisture driven) CO₂ effects should be strictly separated, which requires data to be tested against soil moisture.

Soil moisture dynamics of calcareous grassland under elevated CO2

Water relations of nutrient-poor calcareous grassland under long-term CO₂ enrichment were investigated. Understanding CO₂ effects on soil moisture is critical because productivity in these grasslands is water limited. In general, leaf conductance was reduced at elevated CO₂, but responses strongly depended on date and species. Evapotranspiration (measured as H₂O gas exchange) revealed only small, non-significant reductions at elevated CO₂, indicating that leaf conductance effects were strongly buffered by leaf boundary layer and canopy conductance (leaf area index was not or only marginally increased under elevated CO₂). However, these minute and non-significant responses of water vapour loss accumulated over time and resulted in significantly higher soil moisture in CO₂-enriched plots (gravimetric spot measurements and continuous readings using a network of time-domain reflectometry probes). Differences strongly depended on date, with the smallest effects when soil moisture was very high (after heavy precipitation) and effects were largest at intermediate soil moisture. Elevated CO₂ also affected diurnal soil moisture courses and rewetting of soils after precipitation. We conclude that ecosystem-level controls of the water balance (including soil feedbacks) overshadow by far the physiological effects observed at the leaf level. Indirect effects of CO₂ enrichment mediated by trends in soil moisture will have far-ranging consequences on plant species composition, soil bacterial and faunal activity as well as on soil physical structure and may indirectly also affect hydrology and trace gas emissions and atmospheric chemistry.