Soil Microsites Research Articles

Scale-dependent linkages between nitrate isotopes and denitrification in surface soils: implications for isotope measurements and models.

Natural abundance nitrate (NO3 (-)) isotopes represent a powerful tool for assessing denitrification, yet the scale and context dependence of relationships between isotopes and denitrification have received little attention, especially in surface soils. We measured the NO3 (-) isotope compositions in soil extractions and lysimeter water from a semi-arid meadow and lawn during snowmelt, along with the denitrification potential, bulk O2, and a proxy for anaerobic microsites. Denitrification potential varied by three orders of magnitude and the slope of δ(18)O/δ(15)N in soil-extracted NO3 (-) from all samples measured 1.04±0.12 (R (2)=0.64, p<0.0001), consistent with fractionation from denitrification. However, δ(15)N of extracted NO3 (-) was often lower than bulk soil δ(15)N (by up to 24‰), indicative of fractionation during nitrification that was partially overprinted by denitrification. Mean NO3 (-) isotopes in lysimeter water differed from soil extractions by up to 19‰ in δ(18)O and 12‰ in δ(15)N, indicating distinct biogeochemical processing in relatively mobile water versus soil microsites. This implies that NO3 (-) isotopes in streams, which are predominantly fed by mobile water, do not fully reflect terrestrial soil N cycling. Relationships between potential denitrification and δ(15)N of extracted NO3 (-) showed a strong threshold effect culminating in a null relationship at high denitrification rates. Our observations of (1) competing fractionation from nitrification and denitrification in redox-heterogeneous surface soils, (2) large NO3 (-) isotopic differences between relatively immobile and mobile water pools, (3) and the spatial dependence of δ(18)O/δ(15)N relationships suggest caution in using NO3 (-) isotopes to infer site or watershed-scale patterns in denitrification.

Microsite Differentiation Drives the Abundance of Soil Ammonia Oxidizing Bacteria along Aridity Gradients

Soil ammonia oxidizing bacteria (AOB) and archaea (AOA) are responsible for nitrification in terrestrial ecosystems, and play important roles in ecosystem functioning by modulating the rates of N losses to ground water and the atmosphere. Vascular plants have been shown to modulate the abundance of AOA and AOB in drylands, the largest biome on Earth. Like plants, biotic and abiotic features such as insect nests and biological soil crusts (biocrusts) have unique biogeochemical attributes (e.g., nutrient availability) that may modify the local abundance of AOA and AOB. However, little is known about how these biotic and abiotic features and their interactions modulate the abundance of AOA and AOB in drylands. Here, we evaluate the abundance of amoA genes from AOB and AOA within six microsites commonly found in drylands (open areas, biocrusts, ant nests, grasses, nitrogen-fixing shrubs, and trees) at 21 sites from eastern Australia, including arid and mesic ecosystems that are threatened by predicted increases in aridity. Our results from structural equation modeling suggest that soil microsite differentiation alters the abundance of AOB (but not AOA) in both arid and mesic ecosystems. While the abundance of AOA sharply increased with increasing aridity in all microsites, the response of AOB abundance was microsite-dependent, with increases (nitrogen-fixing shrubs, ant nests), decreases (open areas) or no changes (grasses, biocrusts, trees) in abundance with increasing aridity. Microsites supporting the highest abundance of AOB were trees, nitrogen-fixing shrubs, and ant nests. These results are linked to particular soil characteristics (e.g., total carbon and ammonium) under these microsites. Our findings advance our understanding of key drivers of functionally important microbial communities and N availability in highly heterogeneous ecosystems such as drylands, which may be obscured when different soil microsites are not explicitly considered.

Archaeal ammonia oxidizers respond to soil factors at smaller spatial scales than the overall archaeal community does in a high Arctic polar oasis.

Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2-5 m scale (P < 0.05), whereas AOA communities were dependent at the ∼1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases.

Species-specific effects of temperate trees on greenhouse gas exchange of forest soil are diminished by drought

Tree species identity and root-associated microbes are assumed to play an important role in the global terrestrial fluxes of the key biogenic greenhouse gases (GHG; CO2, CH4, N2O), but the specific processes driving this influence and the importance against abiotic impacts are poorly understood. To what extent changes in the species composition of temperate forests and increases in the frequency and duration of summer droughts in the course of global climate change will alter GHG emissions remains unclear. We analyzed the effect of tree species identity and mycorrhizal association type vs. soil drought on GHG fluxes by conducting a greenhouse experiment with four important deciduous tree species which form either ectomycorrhizal or arbuscular mycorrhizal associations. We combined soil gas flux measurements with analyses of leaf gas fluxes, potential fine root respiration, fine root growth and turnover, and N turnover in soil microsites. Our experiment tests the hypotheses that (1) GHG emissions differ between tree species and mycorrhizal association type mainly due to differences in root activity and root-induced processes, and (2) soil drought decreases the amount of GHG exchange from different tree species to a different extent. We found a two times higher global warming potential (GWP) from soil gas exchange in European ash than in the other three tree species (1.9 vs. 0.8–1.0 g CO2-eq kg−1 h−1) mainly due to much higher root mass-specific CO2 emission rates (495 vs. 210–236 mg C kg−1 h−1). Apart from the influence of species differences in fine root productivity, we show a stronger increase in CO2 emission rates per portion of white roots in ash which may indicate a higher metabolic activity of unsuberized fine roots in this tree species. Ectomycorrhizal tree species differed from arbuscular mycorrhizal tree species by a two times greater increase in CO2 emissions per fine root production. The N2O emissions per root mass were up to five times higher in beech than in the other species, caused either by higher nitrate production in the rhizosphere or by lower nitrate consumption. Soil porosity drove the amount of methane uptake, while biotic influences were subordinate. Soil drought generally exerted an important control on GHG fluxes: low water-filled pore space decreased the GWP from soil emissions by only 9% in sycamore, but by 40% (European beech) to 68% (European ash) in the other tree species and largely diminished any tree species differences. This suggests that tree species identity may substantially alter the GWP of temperate forests through rhizosphere processes, but this influence on GHG exchange is diminished by soil drought.

Does tallgrass prairie restoration enhance the invasion resistance of post-agricultural lands?

There is building interest in the use of ecological restoration to enhance the biotic invasion resistance of disturbed lands. However, few studies have rigorously examined the effect of community restoration on biotic invasion resistance under conditions of controlled invader propagule pressure. Results are presented from a field experiment conducted in a post-agricultural grassland in eastern Kansas to explore the interplay of tallgrass prairie restoration and invader propagule pressure in modulating plant invasion. Seed additions of multiple native and non-native species were used to provide a general test of biotic invasion resistance under varied propagule availability. Restoration increased plant diversity, increased above ground productivity, reduced the availability of light, soil moisture and bare soil microsites and strongly suppressed the invasion of all species sown into the experiment, including the highly invasive exotic legume, Lespedeza cuneata. In the absence of restoration, L. cuneata rapidly dominated plots where it had been sown, particularly at the highest propagule pressure. Results of multiple regression modelling suggested that restoration most likely increased community resistance to L. cuneata invasion through changes in functional guild composition rather than through changes in species diversity. Overall our study indicates that restoration of abandoned agricultural land to native tallgrass prairie can enhance invasion resistance in the face of substantial invader propagule pressures by altering community composition to dominance by native species that are efficient in utilizing resources.

Reducing conditions, reactive metals, and their interactions can explain spatial patterns of surface soil carbon in a humid tropical forest

Humid tropical forests support large stocks of surface soil carbon (C) that exhibit high spatial variability over scales of meters to landscapes (km). Reactive minerals and organo-metal complexes are known to contribute to C accumulation in these ecosystems, although potential interactions with environmental factors such as oxygen (O2) availability have received much less attention. Reducing conditions can potentially contribute to C accumulation, yet anaerobic metabolic processes such as iron (Fe) reduction can also drive substantial C losses. We tested whether these factors could explain variation in soil C (0–10 and 10–20 cm depths) over multiple spatial scales in the Luquillo Experimental Forest, Puerto Rico, using reduced iron (Fe(II)) concentrations as an index of reducing conditions across sites differing in vegetation, topographic position, and/or climate. Fine root biomass and Fe(II) were the best overall correlates of site (n = 6) mean C concentrations and stocks from 0 to 20 cm depth (r = 0.99 and 0.98, respectively). Litterfall decreased as reducing conditions, total and dead fine root biomass, and soil C increased among sites, suggesting that decomposition rates rather than C inputs regulated soil C content at the landscape scale. Strong relationships between Fe(II) and dead fine root biomass suggest that reducing conditions suppressed particulate organic matter decomposition. The optimal mixed-effects regression model for individual soil samples (n = 149) showed that aluminum (Al) and Fe in citrate/ascorbate and oxalate extractions, Fe(II), fine root biomass, and interactions between Fe(II) and Al explained most of the variation in C concentrations (pseudo R2 = 0.82). The optimal model of C stocks was similar but did not include fine root biomass (pseudo R2 = 0.62). In these models, soil C concentrations and stocks increased with citrate/ascorbate-extractable Al and oxalate-extractable Fe. However, soil C decreased with citrate/ascorbate-extractable Fe, an index of Fe susceptible to anaerobic microbial reduction. At the site scale (n = 6), ratios of citrate/ascorbate to oxalate-extractable Fe consistently decreased across a landscape O2 gradient as C increased. We suggest that the impact of reducing conditions on organic matter decomposition and the presence of organo-metal complexes and C sorption by short-range order Fe and Al contribute to C accumulation, whereas the availability of an Fe pool to sustain anaerobic respiration in soil microsites partially attenuates soil C accumulation in these ecosystems.

Response of soil enzyme activity to long-term restoration of desertified land

Low extracellular enzyme activity in desert soil can be recovered during the succession of re-vegetation, especially in soils forming under shrubs (microsite soil), which closely reflects desert restoration conditions. However, not much is known about the restoration of soil enzyme activity at these microsites. By using the space-for-time substitution method, soils on moving sand dunes that had been stabilized at different dates over a fifty year period at the southeastern fringe of the Tengger Desert were selected to investigate the enzyme activities in the surface soil crust and three other soil depths at microsites to demonstrate the evolution of enzymatic activity at different stages from bare soil to complex vegetation over a fifty year sequence. The results showed that organic C and total and available N, P, and enzyme activities (dehydrogenase, catalase, α- and β-glucosidase, protease, and phosphatase) were progressively enhanced in each microsite soil in the 50-year chronosequence and had effect down to 35cm depth. Soil enzyme activities of the crust and the 0–5cm soil layer were higher than in deeper soil layers. The observed increase over time of the values of the measured soil properties, such as organic C, total and available N, was much larger in the crust and the 0–5cm soil layer in comparison to the deeper layers. The improvement of desert soil quality indicated that desertification can be mitigated to a certain extent under human controls.

Aboveground Vegetation and Perennial Grass Seed Bank in Arid Rangelands Disturbed by Grazing

Recruitment by seeds can be an important mechanism for recovery of plant communities following disturbance. Our objective was to assess the density and spatial patterning of perennial grass (highly preferred by herbivores) seeds in litter patches at locations with different aboveground vegetation structure in sites with different grazing history characteristic of the Patagonian Monte (Argentina). We asked whether structural differences in aboveground vegetation are reflected in the density and spatial patterning of perennial grass seeds in litter patches. We selected two study sites characteristic of the Patagonian Monte and within them three locations representing different vegetation states, resulting from different combinations of grazing and/or release from grazing history. At each location, we assessed the density of perennial grass seeds in litter patches at microsites beneath plant patches (canopy) and in interpatch areas without or with scattered vegetation (bare soil) at three dates during the reproductive and seed dispersal periods. The density of perennial grass seeds in litter patches was greater at canopy than at bare soil microsites, and the number of litter patches without seeds increased with decreasing total plant cover at both microsites. The density of perennial grass seeds in litter patches did not vary with differences in total plant cover or litter patch attributes at canopy microsites, while it was reduced with decreasing total plant cover at bare soil microsites. We concluded that differences in aboveground plant cover differentially affected the density of perennial grass seeds in litter patches at contrasting soil microsites. Thus potential microsites for perennial grass recruitment by seeds would increase from litter patches at bare soil microsites to litter patches at canopy microsites at locations with high and low aboveground plant cover, respectively. These issues should be considered for the sustainable management of these rangelands.

The rhizosphere and hyphosphere differ in their impacts on carbon and nitrogen cycling in forests exposed to elevated CO2

While multiple experiments have demonstrated that trees exposed to elevated CO₂ can stimulate microbes to release nutrients from soil organic matter, the importance of root- versus mycorrhizal-induced changes in soil processes are presently unknown. We analyzed the contribution of roots and mycorrhizal activities to carbon (C) and nitrogen (N) turnover in a loblolly pine (Pinus taeda) forest exposed to elevated CO₂ by measuring extracellular enzyme activities at soil microsites accessed via root windows. Specifically, we quantified enzyme activity from soil adjacent to root tips (rhizosphere), soil adjacent to hyphal tips (hyphosphere), and bulk soil. During the peak growing season, CO₂ enrichment induced a greater increase of N-releasing enzymes in the rhizosphere (215% increase) than in the hyphosphere (36% increase), but a greater increase of recalcitrant C-degrading enzymes in the hyphosphere (118%) than in the rhizosphere (19%). Nitrogen fertilization influenced the magnitude of CO₂ effects on enzyme activities in the rhizosphere only. At the ecosystem scale, the rhizosphere accounted for c. 50% and 40% of the total activity of N- and C-releasing enzymes, respectively. Collectively, our results suggest that root exudates may contribute more to accelerated N cycling under elevated CO₂ at this site, while mycorrhizal fungi may contribute more to soil C degradation.

Control of soil phosphatase activities at millimeter scales in a mixed paper birch – Douglas-fir forest: The importance of carbon and nitrogen

Organic P can serve as an important source of P for plants and microbes when mineralized by extracellular phosphatases. Substrate induction, end-product repression and/or resource limitation regulate activities of phosphatase in bulk soils. Yet, factors controlling enzyme activities in fine-scale microsites may differ from those observed at larger scales. Understanding such differences is needed to improve estimates of global models of biogeochemical cycling. Imprinting of soil profiles using cellulose sheets infused with chromogenic substrates allows study of extracellular enzymes at mm scales under naturally occurring soil temperatures, with minimal disturbance to soil microbial communities. In this study, we used a soil imprinting approach to investigate soil chemical characteristics associated with mm-scale regions of high in situ phosphatase activities in a mixed paper birch – Douglas-fir forest in the southern interior of British Columbia. In addition, we tested whether the addition of simple (ammonium chloride plus sodium acetate) and complex (cellulose, collagen, chitin) forms of carbon (C) and/or nitrogen (N) to 1 cm2 microplots on soil profiles influenced in situ phosphatase activity. In unamended microplots, percent C was 30% higher on average (P = 0.05) and percent N was about 15% higher (P = 0.05) in high-phosphatase microsites. Extractable P did not differ between high and low-phosphatase microsites, regardless of the form of P measured. Within the first 24 h, no difference in imprintable phosphatase was observed between C and N addition treatments, but after 72 h, microplots receiving any substrate containing N had higher phosphatase activities than those receiving only water (P < 0.001). The results from both of our studies support a role for resource limitation in regulating phosphatase activities at this site because either (i) P became limiting in microsites with higher amounts of C and N, and/or (ii) microsites with higher C and N were the ones where these nutrients were in sufficient supply to allow microbes to excrete extracellular enzymes. We conclude that phosphatase excretion occurs in C + N-enriched soil microsites, but that any such phosphatase-active microsites located beyond the rhizosphere are unlikely to supply P to roots because of the low diffusion rates of orthophosphate.

Breaking the enzymatic latch: impacts of reducing conditions on hydrolytic enzyme activity in tropical forest soils

The enzymatic latch hypothesis proposes that oxygen (O2) limitation promotes wetland carbon (C) storage by indirectly decreasing the activities of hydrolytic enzymes that decompose organic matter. Humid tropical forest soils are often characterized by low and fluctuating redox conditions and harbor a large pool of organic matter, yet they also have the fastest decomposition rates globally. We tested the enzymatic latch hypothesis across a soil O2 gradient in the Luquillo Experimental Forest, Puerto Rico, USA. Enzyme activities expressed on a soil mass basis did not systematically decline across a landscape O2 gradient, nor did phenolics accumulate, the proposed mechanism of the enzymatic latch. Normalizing enzyme activities by C concentrations did suggest a decline in several enzymes as mean soil O2 decreased. However, relationships between hydrolytic enzymes and reducing conditions were scale‐dependent: enzymes displayed neutral to strongly positive relationships with reducing conditions and phenolics when comparing samples within sites, and enzyme activities in 18‐d anaerobic incubations generally exceeded those in aerobic soils despite a fourfold increase in phenolics. In summary, although O2 availability and the activities of some enzymes appeared to be related at landscape scales after accounting for differences in organic matter, reducing conditions and phenolic compounds did not appear to constrain soil hydrolytic enzyme activity at the scale of soil microsites, challenging the enzymatic latch hypothesis. Hydrolytic enzymes can be resilient to periodic anaerobiosis and may actually stimulate O2 consumption at the microsite scale. We suggest a critical re‐examination of mechanisms and the scale dependence of couplings between O2 and decomposition in terrestrial soils.

A big-microsite framework for soil carbon modeling.

Soil carbon cycling processes potentially play a large role in biotic feedbacks to climate change, but little agreement exists at present on what the core of numerical soil C cycling models should look like. In contrast, most canopy models of photosynthesis and leaf gas exchange share a common 'Farquhaur-model' core structure. Here, we explore why a similar core model structure for heterotrophic soil respiration remains elusive and how a pathway to that goal might be envisioned. The spatial and temporal variation in soil microsite conditions greatly complicates modeling efforts, but we believe it is possible to develop a tractable number of parameterizable equations that are organized into a coherent, modular, numerical model structure. First, we show parallels in insights gleaned from linking Arrhenius and Michaelis-Menten kinetics for both photosynthesis and soil respiration. Additional equations and layers of complexity are then added to simulate substrate supply. For soils, model modules that simulate carbon stabilization processes will be key to estimating the fraction of soil C that is accessible to enzymes. Potential modules for dynamic photosynthate input, wetting-event inputs, freeze-thaw impacts on substrate diffusion, aggregate turnover, soluble-C sorption, gas transport, methane respiration, and microbial dynamics are described for conceptually and numerically linking our understanding of fast-response processes of soil gas exchange with longer-term dynamics of soil carbon and nitrogen stocks.

Microbial community structure varies across soil organic matter aggregate pools during tropical land cover change

Soil microorganisms regulate multiple input and loss pathways of soil carbon (C); hence, changes in microbial communities are expected to affect soil organic matter (SOM) cycling and storage. Despite this, very little is known about how microbes respond to changes in soil structure and vegetation with land use and land cover change. This study aimed to identify relationships between microbial community composition and the distribution of SOM among soil aggregate fractions to answer the following research questions: (1) Are different microbial groups associated with different SOM pools? and (2) How do these relationships differ with changes in vegetation during tropical forest succession? We measured microbial composition via phospholipid fatty acid (PLFA) analysis and C and nitrogen (N) concentrations on physically separated aggregate fractions of soils from pastures, secondary forests (40 and 90 years old) naturally regrowing on abandoned pastures, and reference or primary forests in Puerto Rico. We found different microbial communities associated with different soil aggregate fractions. Fungal to bacterial ratios decreased and gram-positive to gram-negative bacterial ratios increased with decreasing physical fraction size (from the macroaggregates to the silt and clay fractions). Microbial composition also varied with land cover type and forest successional stage, with consistent trends among soil fractions. These results show that the soil matrix and soil microsite properties play an important role in the spatial distribution of fungal and bacterial-dominated communities. The similarities in land cover effects on microbial communities at different spatial scales suggest similar controls may be influencing microbial composition with potential implications for SOM storage and turnover. In addition, the majority of C and N (relative to total soil C and fraction mass) was isolated in the macroaggregate-occluded silt and clay-sized fractions, suggesting that association with mineral surfaces, and not occlusion of particulate organic matter within aggregates, is the dominant stabilization mechanism for SOM in these highly-weathered, fine-textured soils. These results highlight the importance of soil aggregation in C storage but through mechanisms different than those reported for temperate grassland soils.

Ectomycorrhizal fungal hyphae communities vary more along a pH and nitrogen gradient than between decayed wood and mineral soil microsites

Ectomycorrhizal (ECM) fungal community composition is structured by soil properties, but specialization for woody microsites by ECM fungi is equivocal. Because fungal mycelia explore the substrate and colonize nutrient patches, studies targeting ECM fungal hyphae may reveal niche preferences. Moreover, studying the distribution and composition of ECM fungal hyphal communities contributes to our understanding of nutrient cycling in forest soils. We used next-generation sequencing to determine whether the composition of forest floor fungal communities present as hyphae differed among three microsite types: decayed wood, mineral soil adjacent to intact logs, or control mineral soil of mature spruce forests in British Columbia. The microsites were located in three blocks that were separated by 1 km and varied in elevation. Across the site, the ECM fungal lineage /amphinema–tylospora was the most operational taxonomic unit (OTU)-rich group, while the saprotrophic order Mortierellales was also dominant. ECM fungal species differed among microsites. For example, ECM fungal OTUs identified as Tylospora fibrillosa and Russula curtipes were more frequent in decayed wood as compared with control mineral soil. However, ECM fungal communities were more strongly structured by block characteristics, and we conclude there is no distinct group of ECM fungi specializing in the soil microsites examined in this forest.

Early season dynamics of soil nitrogen fluxes in fertilized and unfertilized boreal forests

The supply of soil nitrogen (N) for plant uptake largely controls plant growth and has a major impact on a wide range of biogeochemical processes in terrestrial ecosystems. The soil solution typically contains a large variety of N forms and recent evidence suggests that the share of amino acids to soil N fluxes dominates over inorganic N in boreal forest soils. In this study we applied a microdialysis technique to investigate in-situ induced diffusive fluxes across microdialysis membranes (FMD) in fertilized and non-fertilized boreal forest sites in early spring, at the onset of plant growth. We studied temporal shifts of FMD at short (minutes to hours) and prolonged time-scales (hours to days). We also estimated N pools in soil water and KCl extracts and critically evaluated the significance of results depending on the method chosen. Our results indicate that FMD of boreal forest soil is dominated by amino acids in early spring and that growing roots should encounter the full range of organic and inorganic N forms in these soils. In contrast, soil water and KCl extracts were dominated by NH4+. Some amino acids displayed rapidly declining FMD (<1 h) possibly due to the rapid formation of a depletion zone near the membrane surface but the FMD of most amino acids remained high and unchanged over extended periods of dialysis indicating that these soils provide a continuous supply of amino acids for root uptake. Forest fertilization with NH4NO3 led to a significant increase in FMD of NO3− and NH4+, with FMD of NH4+ but not of NO3− remaining high for prolonged time. A separate trial with addition of NO3− showed a significantly slower decline of FMD in soils of previously fertilized forests compared to unfertilized forests, suggesting biological immobilization being a major cause of rapid decline of nitrate fluxes. Our results corroborate earlier studies suggesting amino acids to be a significant fraction of plant available N in boreal forests. They also suggest that, besides inorganic N, roots may encounter a wide spectrum of amino acids after intercepting new soil microsites and that most, but not all, amino acids may be constantly replenished at the root surface. Further, from our results we conclude that detailed insights into in-situ N dynamics of soils can be gained through microdialysis.

Evidence for spatially inaccessible labile N from a comparison of soil core extractions and soil pore water lysimetry

NH4+, NO3−, and amino acids are generally thought to be either mobile in the soil solution or adsorbed to ion exchange sites on soil surfaces. Here we examine a third possibility: some labile N compounds may be spatially inaccessible to plants and microbes due to isolation in soil microsites with low water potential. We tested this hypothesis in Arctic tussock tundra soils by comparing soil NH4+, NO3−, and amino acid concentrations using tension lysimetry, water extractions, and salt extractions. We used lysimeters to measure labile N that is in the mobile soil solution, and water extracts and salt extracts as combined measurements of mobile, adsorbed, and spatially inaccessible labile N. Averaged through the 2011 growing season, 37 ± 28% of labile N was adsorbed to ion exchange sites, 10 ± 4% was in the mobile soil solution, and the remaining 52 ± 26% was neither mobile nor on exchange sites. Labile N concentrations in water extractions were, on average, ∼5 times higher than those in lysimeters. These results suggest that a large quantity of the water-extractable N is not available in the mobile soil solution. The estimated quantity of spatially inaccessible labile N declined over the course of the season, suggesting that these pools can be gradually drawn down by plant or microbial uptake. To place these results in context, we reviewed published labile N concentrations in lysimeters and extractions in other ecosystems and these published values were consistent with our results, showing much higher concentrations of labile N in extractions than in lysimeters. Overall, our study supports the hypothesis that soils can contain a substantial spatially inaccessible pool of extractable labile N that is not immediately available to plants and soil microbes.

Quantification of N2O emission pathways via a 15N tracing model

A 15N tracing model was developed to analyse nitrous oxide (N2O) dynamics in terrestrial ecosystems, which build on previous tracing models for the quantification of the main mineral nitrogen (N) transformations and soil nitrite (NO2−) dynamics. The N2O dynamics in the model are directly associated with three NO2− sub-pools. Four pathways for N2O production in soil were considered in the model: i) reduction of NO2− associated with nitrification (NO2−nit → N2Onit), ii) reduction of NO2− associated with denitrification (NO2−den → N2Oden), iii) reduction of NO2− associated with organic N (Norg) oxidation (NO2−org → N2Oorg), and iv) codenitrification (N2Ocod), a hybrid reaction where one N atom in N2O originates from organic N and the other from NO2−den. Soil N2O can further be reduced to N2 and/or can be emitted to the atmosphere. The reaction kinetics and emission notations are based on first-order approaches. Parameter optimization was carried out with a Markov Chain Monte Carlo (MCMC) technique that is suitable for models with large number of parameters. The 15N tracing tool was tested with a data set from a 15N tracing study on grassland soil. Tracing model results showed that on average over a 12 day period N2Onit, N2Oden, N2Oorg and N2Ocod contributed 9%, 20%, 54% and 18% to the total N2O emission, respectively. The results are in line with estimates based on analytical approaches that consider three N2O emission pathways. The strength of this new 15N tracing tool is that for the first time four N2O emission pathways, including a hybrid-reaction, can simultaneously be quantified. The analysis highlights that heterotrophic processes related to organic N turnover and neither autotrophic nitrification nor denitrification may be the prevailing pathways for N2O production in old grassland soil. The underlying NO2− and N2O reduction kinetics are in agreement with denitrification gene expressions and the calculated N2/N2O ratios are in the expected range. The tracing model provides insights on N dynamics which may occur in soil microsites. This information is important for the development of more realistic representations of soil N cycling in ecosystem models.

Emissions of CH4, CO2, and N2O from soil at a cattle overwintering area as affected by available C and N

Relationships between CH4, CO2, and N2O emissions were studied in soil that had been freshly amended with large deposits of cattle wastes. Dynamics of CH4, CO2, and N2O emissions were investigated with flux chambers from early April to late June 2011, during the 3 months following cattle overwintering at the site. This 81-day field study was supplemented with soil analyses of available C and N content and measurement of denitrification activity. In a more detailed field investigation, the daily time course of emissions was determined. The field research was complemented with a laboratory experiment that focused on the short-term time course of N2O and CH4 production in artificially created anoxic soil microsites. The following hypotheses were tested: (i) a large input of C (and N and other nutrients) in cattle manure creates conditions suitable for methanogenesis, and therefore overwintering areas can produce large amounts of CH4; (ii) N2O is produced and emitted until the level of mineral N decreases, while the level of CH4 production is low; and (iii) production of CH4 is greater when N immobilization decreases the level of NO3− in soil. N2O emissions were relatively large during the first 3 weeks, then peaked (at ca. 4000μgN2ONm−2h−1) and soon decreased to almost zero; the changes were related to the mineral and soluble organic N content in soil. CH4 fluxes were large, though variable, in the first 2 months (600–3000μgCH4Cm−2h−1) and were independent of C and N availability. Although time courses differed for CH4 and N2O, a negative relationship between N2O and CH4 emissions was not detected. Contrary to CH4 and N2O fluxes, CO2 emissions progressively increased to ca. 300mgCO2Cm−2h−1 at the end of the field study and were closely related to air and soil temperatures. Diurnal measurements revealed significant correlations between temperature and emissions of CH4, N2O, and CO2. Addition of C to soil during anaerobic incubation increased the production and consumption of N2O and supported the emission of CH4. The results suggest that rapid denitrification significantly contributes to the exhaustion of oxidizing agents and helps create microsites supporting methanogenesis in otherwise N2O-producing upland soil. The results also indicate that accurate estimate of gas fluxes in animal-impacted grassland areas requires assessment of both diurnal and long-term changes in CH4, CO2, and N2O emissions.

Implications of Environmental Stress during Seed Development on Reproductive and Seed Bank Persistence Traits in Wild Oat (Avena fatua L.)

Weeds produce seed under a wide range of conditions, depending on timing of emergence, prevailing crop, soil microsites, and climatic conditions, among other factors. We hypothesized that the maturation environment during weed seed development will influence reproductive allocation and seed persistence traits, such as seed dormancy and vigor, and needs to be considered when formulating weed management strategies. This research evaluated the effects of shade and drought stress on reproductive allocation, seed dormancy and seed vigor in select lines of wild oat (Avena fatua L.). Plants were grown in the greenhouse under drought stress and shade. Harvested seed were subjected to controlled after-ripening and aging regimes. Drought and shade reduced reproductive allocation and resulted in seed with less intense primary dormancy compared to the plants grown under resource-rich conditions, but had no apparent effect on seed vigor. Our data provide additional support to the hypothesis that seed dormancy within a species is a highly plastic trait that can be strongly influenced by the growth conditions of the mother plant. Such plasticity may have important implications for establishing ecologically-based weed control criteria on which threshold-based weed management systems are implemented.

Nitrogen, organic carbon and sulphur cycling in terrestrial ecosystems: linking nitrogen saturation to carbon limitation of soil microbial processes

Elevated and chronic nitrogen (N) deposition to N-limited terrestrial ecosystems can lead to ‘N saturation’, with resultant ecosystem damage and leaching of nitrate (NO3 −) to surface waters. Present-day N deposition, however, is often a poor predictor of NO3 − leaching, and the pathway of the ecosystem transition from N-limited to N-saturated remains incompletely understood. The dynamics of N cycling are intimately linked to the associated carbon (C) and sulphur (S) cycles. We hypothesize that N saturation is associated with shifts in the microbial community, manifest by a decrease in the fungi-to-bacteria ratio and a transition from N to C limitation. Three mechanisms could lead to lower amount of bioavailable dissolved organic C (DOC) for the microbial community and to C limitation of N-rich systems: (1) Increased abundance of N for plant uptake, causing lower C allocation to plant roots; (2) chemical suppression of DOC solubility by soil acidification; and (3) enhanced mineralisation of DOC due to increased abundance of electron acceptors in the form of $${{\text{SO}}_{ 4}}^{ 2-}$$ and NO3 − in anoxic soil micro-sites. Here we consider each of these mechanisms, the extent to which their hypothesised impacts are consistent with observations from intensively-monitored sites, and the potential to improve biogeochemical models by incorporating mechanistic links to the C and S cycles.