Is vegetation composition or soil chemistry the best predictor of the soil microbial community?

With the species composition and/or functioning of many ecosystems currently changing due to anthropogenic drivers it is important to understand and, ideally, predict how changes in one part of the ecosystem will affect another. Here we assess if vegetation composition or soil chemistry best predicts the soil microbial community. The above and below-ground communities and soil chemical properties along a successional gradient from dwarf shrubland (moorland) to deciduous woodland (Betula dominated) were studied. The vegetation and soil chemistry were recorded and the soil microbial community (SMC) assessed using Phospholipid Fatty Acid Extraction (PLFA) and Multiplex Terminal Restriction Fragment Length Polymorphism (M-TRFLP). Vegetation composition and soil chemistry were used to predict the SMC using Co-Correspondence analysis and Canonical Correspondence Analysis and the predictive power of the two analyses compared. The vegetation composition predicted the soil microbial community at least as well as the soil chemical data. Removing rare plant species from the data set did not improve the predictive power of the vegetation data. The predictive power of the soil chemistry improved when only selected soil variables were used, but which soil variables gave the best prediction varied between the different soil microbial communities being studied (PLFA or bacterial/fungal/archaeal TRFLP). Vegetation composition may represent a more stable ‘summary’ of the effects of multiple drivers over time and may thus be a better predictor of the soil microbial community than one-off measurements of soil properties.     

Measurement of the apparent diffusion coefficient of N‐butane in soil

Measurements of in‐soil diffusion coefficients and the application of an appropriate diffusional model can allow for a more accurate prediction of soil gas concentrations and movement to locate subterranean contamination of volatile materials. The present study was undertaken to measure and evaluate the “apparent in‐soil diffusion coefficient”; for n‐butane through soil columns under non‐steady‐state conditions. The term “apparent in‐soil diffusion coefficient”; refers to a numerical coefficient that primarily describes the movement of the material by diffusion but also contains effects due to other mechanisms (e.g., adsorption and solubility).

Six test columns were evaluated at three soil porosity levels ranging from 0.30 to 0.43 and at two column temperature conditions, nominally 18°C and 7°C. Soil columns measured 25.4 cm in diameter by 84 cm in height and contained a moist sand/silt/clay mixture. The numerical range for the apparent in‐soil diffusion coefficients for n‐butane was 0.447 × 10^‐3cm²/s to 0.561 × 10^‐3cm²/s. The lower coefficient values were associated with lower soil porosity levels and cooler column conditions.     

Plant–soil feedbacks and the coexistence of competing plants

Plant–soil feedbacks can have important implications for the interactions among plants. Understanding these effects is a major challenge since it is inherently difficult to measure and manipulate highly diverse soil communities. Mathematical models may advance this understanding by making the interplay of the various processes affecting plant–soil interaction explicit and by quantifying the relative importance of the factors involved. The aim of this paper is to provide a complete analysis of a pioneering plant–soil feedback model developed by Bever and colleagues (J Ecol 85: 561–573, 1997; Ecol Lett 2: 52–62, 1999; New Phytol 157: 465–473, 2003) to fully understand the range of possible impacts of plant–soil feedbacks on plant communities within this framework. We analyze this model by means of a new graphical method that provides a complete classification of the potential effects of soil communities on plant competition. Due to the graphical character of the method, the results are relatively easy to obtain and understand. We show that plant diversity depends crucially on two key parameters that may be viewed as measures of the intensity of plant competition and the direction and strength of plant–soil feedback, respectively. Our analysis provides a formal underpinning of earlier claims that plant–soil feedbacks, especially when they are negative, may enhance the diversity of plant communities. In particular, negative plant–soil feedbacks can enhance the range of plant coexistence by inducing competitive oscillations. However, these oscillations can also destabilize plant coexistence, leading to low population densities and extinctions. In addition, positive feedbacks can allow locally stable forms of plant coexistence by inducing alternative stable states. Our findings highlight that the inclusion of plant–soil interactions may fundamentally alter the predictions on the structure and functioning of above-ground ecosystems. The scenarios presented in this study can be used to formulate hypotheses about the ways soil community effects may influence plant competition that can be tested with empirical studies. This will advance our understanding of the role of plant–soil feedback in ecological communities.     

Is the isotopically exchangeable phosphate of a loamy soil the plant-available P?

Carduus nutans L. is an invasive pasture/grassland species which may undergo rapid population growth through positive feedback. Plants ofC. nutans produce a vegetative rosette, and after several months produce stems containing flower-heads, during which time the rosette leaves die and decompose. We investigated the influence ofC. nutans on the nitrogen-fixation ability ofTrifolium repens L. in three experiments. The first experiment was set up in a mixture design, and demonstrated that seedlings ofT. repens were more susceptible to competition with otherT. repens seedlings than toC. nutans seedlings. Nodule numbers and acetylene reduction per unit root, and acetylene reduction per unit nodules were adversely affected by increasingT. repens, but notC. nutans densities. The second experiment was of an additive design, with separate partitions to isolate above-ground and below-ground interference. FloweringC. nutans plants strongly inhibitedT. repens root growth, nodulation and acetylene reduction, but usually only when shoot interference was permitted. This appears to be due to decomposition of rosette leaves, which was maximal at this stage. The third experiment involved monitoring effects of taggedC. nutans individuals againstT. repens in the field. This experiment showed that acetylene reduction was severely influenced by floweringC. nutans (when rosette leaves were decomposing), even when only mild reduction ofT. repens growth was observed, and these effects persisted for some months after theC. nutans plants had died. The results of these experiments in combination suggest that decomposing rosette leaves have a strong potential to inhibitT. repens nitrogen fixation. It appears that allelopathy is involved, since alternative explanations (e.g. root competition byC. nutans; effects ofC. nutans on soil moisture, microbial nutrient immobilisation and light availability; facilitation of herbivores byC. nutans) can be effectively discounted. Although invasive species are often assumed to be associated with soil nitrogen build-up, we believe that some invasive species such asC. nutans have the potential to induce long-term decline of soil nitrogen input.     

Explaining the variation in the soil microbial community: do vegetation composition and soil chemistry explain the same or different parts of the microbial variation?

Aim

To assess whether vegetation composition and soil chemistry explain the same or different parts of the variation in the soil microbial community (SMC).

Method

The above and below-ground communities and soil chemical properties were studied along a successional gradient from moorland to deciduous woodland. The SMC was assessed using PLFAs and M-TRFLPs. Using variance partitioning, Co-Correspondence Analysis (CoCA) and Canonical Correspondence Analysis (CCA), the variation (total inertia) in the SMC was partitioned into variation which was uniquely explained by either plant composition or soil chemistry, variation explained by both soil chemistry and plant composition, and unexplained variation.

Results

Plant community composition uniquely explained 30, 13, 16 and 20% of the inertia and soil chemistry uniquely explained 5, 18, 9 and 9% of the inertia in the archaeal TRFLPs, bacterial TRFLPs, fungal TRFLPs and all PLFAs, respectively.

Conclusion

For the first time, variance partitioning was used to include data from a CoCA; although the current limits of such an approach are shown, this study illustrates the potential of such analyses and shows that soil chemistry and plant composition are, in substantial amounts, explaining different parts of the variation within the SMC. This marks an important step in furthering our understanding of the relative importance of different drivers of change in the SMC.     

What is the effect of soil use on ant communities?

Studies on ant communities in agroecosystems have contributed to the knowledge of the effect of agricultural activities on biological communities. The aim of this study is to explain the effect of soil use on ant communities. We tested the hypothesis that there was a decrease in ant species richness and a change in the species composition at habitats with more intense soil use. We collected ants using sardine baits, subterranean traps and direct sampling at four habitats with different soil use (secundary forest, Acacia forestry, initial stage of succession and mixed crops). The ant species richness did not decrease with intensity of soil use. In successional habitat the species numbers collected using sardine baits and subterranean traps were significantly different. Species composition of communities had a pronounced variation, with the epigaeic and hypogaeic ant faunas of the habitat with high intense soil use (mixed crops) had low similarity with ant communities of the three other habitats. The predator species were restricted to habitats with low intensity of soil use. Then, species composition could better reflect the functional changes on ant communities than species richness. Our data can help to choose the component of ant community that better reflect the response of biodiversity to agricultural impacts.     

Does doping with aluminum alter the effects of ZnO nanoparticles on the metabolism of soil pseudomonads?

Doping of ZnO nanoparticles (NPs) is being used to increase their commercialization in the optical and semiconductor fields. This paper addresses whether doping with Al alters how ZnO NPs at nonlethal levels modifies the metabolism of soil-borne pseudomonads which are beneficial in performing bioremediation or promoting plant growth. The differences in X-ray diffraction (XRD) patterns, observed between commercial ZnO and Al-doped ZnO NPs indicated the aluminum was present as Al NPs. Both particles aggregated in the bacterial growth medium and formed colloids of different surface charges. They had similar effects on bacterial metabolism: rapid, dose-dependent loss in light output indicative of temporary toxicity in a biosensor constructed in Pseudomonas putida KT2440; increased production of a fluorescent pyoverdine-type siderophore, and decreased levels of indole acetic acid and phenazines in Pseudomonas chlororaphis O6. Solubilization of Zn and Al from the NPs contributed to these responses to different extents. These findings indicate that Al-doping of the ZnO NPs did not reduce the ability of the NPs to alter bacterial metabolism in ways that could influence performance of the pseudomonads in their soil environment.     

Does the removal of snowpack and the consequent changes in soil frost affect the physiology of Norway spruce needles?

Climate change may cause a decrease in snow cover in northern latitudes. This, on the other hand, may result in more severe soil frost even in areas where it is not common at present, and may lead to increased stress on the tree canopy. We studied the effects of snow removal and consequent changes in soil frost and water content on the physiology of Norway spruce (Picea abies [L.] Karst.) needles and implications on root biomass. The study was conducted at a 47-year-old Norway spruce stand in eastern Finland during the two winters of 2005/06 and 2006/07. The treatments in three replicates were: (i) natural snow accumulation and melting (CTRL), (ii) artificial snow removal during the winter (OPEN), and (iii) the same as OPEN, but the ground was insulated in early spring to delay soil thawing (FROST). In spite of the deeper soil frost in the OPEN than in the CTRL treatment, soil warming in spring occurred at the same time, whereas soil warming in the FROST was delayed by 2 and 1.5 months in 2006 and 2007, respectively. The soil water content was affected by snow manipulations, being at a lower level in the OPEN and FROST than CTRL in spring and early summer. The physiological measurements of the needles (e.g. starch, carbon and nitrogen content and apoplastic electrical resistance) showed differences between soil frost treatments. The differences were mostly seen between the CTRL and FROST, but also in the case of the starch content in early spring 2007 between the CTRL and OPEN. The needle responses in the FROST were more evident after the colder winter of 2006. The physiological changes seemed to be related to the soil temperature and water content in the early growing season rather than to the wintertime soil temperature. No difference was found in the fine root (diameter < 2 mm) biomass between the treatments assessed in 2007. In the future, conditions similar to the OPEN treatment may be more common than at present in areas experiencing a thick snow cover. The present experiment took place over the course of two years. It is possible that whenever thin snow cover occurs yearly, the reduced starch content during the early spring may be reflected in the tree growth itself as a result of reduced energy reserves.     

Spatial structure of the soil seed bank of Poa annua L.—alien species in the Antarctica

Poa annua L. (annual bluegrass) is the only non–native flowering plant species that has successfully established a breeding population in the maritime Antarctic and has been shown to maintain a soil seed bank. The characteristic of the spatial structure of the Antarctic population of this species is the formation of distinct dense clumps—tussocks. In the temperate zone the species is only loosely tufted. We focused on the characteristics of seed deposition associated with the tussocks and some aspects of the spatial heterogeneity of the soil seed bank of P. annua in the Antarctic. We wanted to assess the microspatial structure of the soil seed bank of annual bluegrass at Arctowski Station. Therefore we compared the number of seeds deposited underneath and in the vicinity of P. annua clumps. Our results indicate that P. annua in the Antarctic maintains a soil seed bank comparable to species typical for the polar tundra. The microspatial structure of P. annua soil seed bank in the Antarctic is highly associated with the presence of tussocks. Seeds are deposited underneath the tussock rather than in the vicinity of the clump. Our results also indicate that seeds are able to survive the Antarctic winter and readily germinate under optimal conditions.     

Does the temperature sensitivity of decomposition of soil organic matter depend upon water content,soil horizon,or incubation time?

Several studies have shown multiple confounding factors influencing soil respiration in the field, which often hampers a correct separation and interpretation of the different environmental effects on respiration. Here, we present a controlled laboratory experiment on undisturbed organic and mineral soil cores separating the effects of temperature, drying–rewetting and decomposition dynamics on soil respiration. Specifically, we address the following questions:

• 1 Is the temperature sensitivity of soil respiration (Q₁₀) dependent on soil moisture or soil organic matter age (incubation time) and does it differ for organic and mineral soil as suggested by recent field studies.
• 2 How much do organic and mineral soil layers contribute to total soil respiration?
• 3 Is there potential to improve soil flux models of soil introducing a multilayer source model for soil respiration?

Eight organic soil and eight mineral soil cores were taken from a Norway spruce (Picea abies) stand in southern Germany, and incubated for 90 days in a climate chamber with a diurnal temperature regime between 7 and 23°C. Half of the samples were rewetted daily, while the other half were left to dry and rewetted thereafter. Soil respiration was measured with a continuously operating open dynamic soil respiration chamber system. The Q₁₀ was stable at around 2.7, independent of soil horizon and incubation time, decreasing only slightly when the soil dried. We suggest that recent findings of the Q₁₀ dependency on several factors are emergent properties at the ecosystem level, that should be analysed further e.g. with regard to rhizosphere effects. Most of the soil CO₂ efflux was released from the organic samples. Initially, it averaged 4.0 μmol m^?2 s^?1 and declined to 1.8 μmol m^?2 s^?1 at the end of the experiment. In terms of the third question, we show that models using only one temperature as predictor of soil respiration fail to explain more than 80% of the diurnal variability, are biased with a hysteresis effect, and slightly underestimate the temperature sensitivity of respiration. In contrast, consistently more than 95% of the diurnal variability is explained by a dual‐source model, with one CO₂ source related to the surface temperature and another CO₂ source related to the central temperature, highlighting the role of soil surface processes for ecosystem carbon balances.     

Retention of phytosiderophores by the soil solid phase – adsorption and desorption

Plant and Soil - Graminaceous plants exude phytosiderophores (PS) for acquiring Fe. Adsorption of PS and its metal complexes to the soil solid phase reduces the FePS solution concentration and...     

Plants‐associated microflora and the remediation of oil‐contaminated soil

The use of plants and their rhizospheric microorganisms is a promising emerging technology for remediating contaminated soils. The degradation of total petroleum hydrocarbon (TPH) in the rhizospheric and nonrhizospheric soil of three domestic plants, namely, alfalfa (Medicaga sativa) broad beans (Vicia faba) and ryegrass (Lolium perenne) was investigated. The experimental data from the studies of plantmicrobe‐soil interactions implicated the enhancement of TPH degradation by the rhizospheric microbial community. Although the three domestic plants exhibited normal growth in the presence of ～1.0% TPH, the degradation was more profound in the case of leguminous plants. The TPH degradation in the soil cultivated with broad beans and alfalfa was 36.6 and 35.8%, respectively, compared with 24% degradation in case of ryegrass. Such a high correlation between plant type and TPH degradation rates indicate that selection for enhanced rhizosphere degradation may be accomplished by selecting leguminous plants.     

Some progress in the study of plant–soil interactions in China

Plants and soil are the base for sustainably surviving human beings on the globe as the role of materials, energy, resources and environment (Shao & Chu 2008; Shao et al. 2008, 2009, 2010, 2012a,b; Liu & Shao, 2010; Ruan et al. 2010; Xu et al. 2010, 2012; Shao 2012; Huang et al. 2013). This topic has been extensively investigated for 100 years with more achievements in many sectors and practical significance in conducting high-efficient agriculture and eco-environmental construction. The plant–soil interaction is the core issue of this topic, which has been given much attention for the past 30 years (Wu et al. 2007, 2010; Zhang et al. 2011, 2013; Xu et al. 2012, 2013).     

Can soil temperature direct the composition of high arctic plant communities?

Abstract. Low temperatures exert a primary constraint on the growth of high arctic vascular plants. However, investigations into the impact of temperature on high arctic plants rarely separate out the role of air and soil temperatures, and few data exist to indicate whether soil temperatures alone can significantly influence the growth of high arctic vascular plants in a manner that might direct community composition. We examined the response of high arctic plants of three functional types (grasses, sedges/rushes and non‐graminoids) to manipulated soil temperature under common air temperature conditions. Target plants, within intact soil cores, were placed in water baths at a range of temperatures between 4.9 and 15.3 °C for one growing season. Grasses responded most rapidly to increased soil temperature, with increased total live plant mass, above‐ground live mass and total below‐ground live mass, with non‐graminoids having the lowest, and sedges/rushes an intermediate degree of response. The ratio of above‐ground live mass to total live mass increased in all growth forms. Grasses, in particular, responded to enhanced soil temperatures by increasing shoot size rather than shoot number. In all growth forms the mass of root tissue beneath the moss layer increased significantly and to a similar extent with increasing soil temperature. These results clearly indicate that different growth forms, although collected from the same plant community, respond differently to changes in soil temperature. As a consequence, factors influencing soil temperature in high arctic ecosystems, such as global climate change or herbivory (which leads to reduced moss depth and increased soil temperatures), may also direct changes in vascular plant community composition.     

DenNit – Experimental analysis and modelling of soil N2O efflux in response on changes of soil water content, soil temperature, soil pH, nutrient availability and the time after rain event

To quantify the effects of soil temperature (T_soil), and relative soil water content (RSWC) on soil N₂O emission we measured N₂O soil efflux with a closed dynamic chamber in situ in the field and from soil cores in a controlled climate chamber experiment. Additionally we analysed the effect of soil acidity, ammonium, and nitrate concentration in the field. The analysis was performed on three meadows, two bare soils and in one forest. We identified soil water content, soil temperature, soil nitrogen content, and pH as the main parameters influencing soil N₂O emission. The response of N₂O emission to soil temperature and relative soil water content was analysed for the field and climate chamber measurements. A non-linear regression model (DenNit) was developed for the field data to describe soil N₂O efflux as a function of soil temperature, soil moisture, pH value, and ammonium and nitrate concentration. The model could explain 81% of the variability in soil N₂O emission of all individual field measurements, except for data with short-term soil water changes, namely during and up to 2 h after rain stopped. We validated the model with an independent dataset. For this additional meadow site 73% of the flux variation could be explained with the model.     

Radiocaesium in an organic soil and the effect of treatment with the fungicide ‘Captan’

Soil fungi accumulate radiocaesium from contaminated soil and it has been hypothesised that this may alter the plant availability and movement of the radionuclide in soil. The effect of twice-monthly addition of an aqueous suspension of the fungicide ‘Captan’ on the changes in a peaty podzol soil at 2 sites, contaminated 2 or 3 years earlier by the injection of ¹³⁴Cs, has been quantified. The sites had different soil acidity and vegetation cover. The less acid soil (pH_water 5.0) had been improved by the addition of lime and fertilizer and was reseeded with grass and clover. The more acid soil (pH_water 3.8) was under hill grasses, herbs and heather. On both sites the addition of fungicide did not alter the amount or concentration of radiocaesium in plant material sampled monthly or the depth distribution of radiocaesium in the soil profile. The concentration of the fungal constituent, ergosterol, in the soil, measured monthly, was unaffected by the fungicide treatment but evidence was obtained from a pot experiment to show that ergosterol decomposes slowly in cold, wet soils. On the more acid soil, two weeks after the last application of fungicide, there was a decline in active fungi as measured by fluorescein diacetate staining. Chloroform fumigation of the more acid soil resulted in a small increase in the amount of ¹³⁴Cs exchangeable with 1 M ammonium acetate. Radiocaesium in seven different fungi grown in pure culture was found to be almost entirely extractable (> 95%) with 1 M ammonium acetate. Another, Amanita rubescens, showed some retention and 88% was extractable. These findings do not preclude the fungal biomass as an important soil component controlling plant availability of radiocaesium from acid, organic soils by maintaining radiocaesium in a biological cycle, but make it unlikely that any fixation by fungi in a chemical sense is involved.