Relative role of deterministic and stochastic determinants of soil animal community: a spatially explicit analysis of oribatid mites

1. Ecologists are debating the relative role of deterministic and stochastic determinants of community structure. Although the high diversity and strong spatial structure of soil animal assemblages could provide ecologists with an ideal ecological scenario, surprisingly little information is available on these assemblages.
2. We studied species-rich soil oribatid mite assemblages from a Mediterranean beech forest and a grassland. We applied multivariate regression approaches and analysed spatial autocorrelation at multiple spatial scales using Moran's eigenvectors. Results were used to partition community variance in terms of the amount of variation uniquely accounted for by environmental correlates (e.g. organic matter) and geographical position. Estimated neutral diversity and immigration parameters were also applied to a soil animal group for the first time to simulate patterns of community dissimilarity expected under neutrality, thereby testing neutral predictions.
3. After accounting for spatial autocorrelation, the correlation between community structure and key environmental parameters disappeared: about 40% of community variation consisted of spatial patterns independent of measured environmental variables such as organic matter. Environmentally independent spatial patterns encompassed the entire range of scales accounted for by the sampling design (from tens of cm to 100 m). This spatial variation could be due to either unmeasured but spatially structured variables or stochastic drift mediated by dispersal. Observed levels of community dissimilarity were significantly different from those predicted by neutral models.
4. Oribatid mite assemblages are dominated by processes involving both deterministic and stochastic components and operating at multiple scales. Spatial patterns independent of the measured environmental variables are a prominent feature of the targeted assemblages, but patterns of community dissimilarity do not match neutral predictions. This suggests that either niche-mediated competition or environmental filtering or both are contributing to the core structure of the community. This study indicates new lines of investigation for understanding the mechanisms that determine the signature of the deterministic component of animal community assembly.

Soil Moisture Deficit as a predictor of the trend in soil water status of grass fields

Nutrient loss from agricultural land following organic fertilizer spreading can lead to eutrophication and poor water quality. The risk of pollution is partly related to the soil water status during and after spreading. In response to these issues, a decision support system (DSS) for nutrient management has been developed to predict when soil and weather conditions are suitable for slurry spreading. At the core of the DSS, the Hybrid Soil Moisture Deficit (HSMD) model estimates soil water status relative to field capacity (FC) for three soil classes (well, moderately and poorly drained) and has potential to predict the occurrence of a transport vector when the soil is wetter than FC. Three years of field observation of volumetric water content was used to validate HSMD model predictions of water status and to ensure correct use and interpretation of the drainage classes. Point HSMD model predictions were validated with respect to the temporal and spatial variations in volumetric water content and soil strength properties. It was found that the HSMD model predictions were well related to topsoil water content through time, but a new class intermediate between poor and moderate, perhaps ‘imperfectly drained’, was needed. With correct allocations of a field into a drainage class, the HSMD model predictions reflect field scale trends in water status and therefore the model is suitable for use at the core of a DSS.

Insignificant impact of prescribed fire on surface soil in a Pinus pinaster plantation, northern Portugal

Following a prescribed fire in a Pinus pinaster forest site located in the north-west Portugal, monitoring of any changes in selected soil characteristics and soil hydrology was undertaken to assess the effects of burning on the following: pH, electrical conductivity, water content, organic carbon and porosity. Thirty plots were established on a regular grid. At each sample plot before and after the fire, samples were collected (disturbed samples from depths of 0-1cm and 1-5cm; undisturbed core samples from 0-5cm). The results indicate that there was no measurable impact on the properties of the soil following this carefully conducted prescribed fire. The fire only affected the litter layer, as intended. Confirmation of this minimal impact on the soil was provided by regrowth of grasses and herbs already occurring two months after the fire. The implication is, therefore, that provided this wildfire-risk reduction strategy is carried out under existing strict guidelines, any impact on soil quality will be minimal.

Effects of Soil Compaction and Organic Carbon Content on Preferential Flow in Loamy Field Soils

Abstract: Preferential flow and transport through macropores affect plant water use efficiency and enhance leaching of agrochemicals and the transport of colloids, thereby increasing the risk for contamination of groundwater resources. The effects of soil compaction, expressed in terms of bulk density (BD), and organic carbon (OC) content on preferential flow and transport were investigated using 150 undisturbed soil cores sampled from 15 × 15–m grids on two field sites. Both fields had loamy textures, but one site had significantly higher OC content. Leaching experiments were conducted in each core by applying a constant irrigation rate of 10 mm h−1 with a pulse application of tritium tracer. Five percent tritium mass arrival times and apparent dispersivities were derived from each of the tracer breakthrough curves and correlated with texture, OC content, and BD to assess the spatial distribution of preferential flow and transport across the investigated fields. Soils from both fields showed strong positive correlations between BD and preferential flow. Interestingly, the relationships between BD and tracer transport characteristics were markedly different for the two fields, although the relationship between BD and macroporosity was nearly identical. The difference was likely caused by the higher contents of fines and OC at one of the fields leading to stronger aggregation, smaller matrix permeability, and a more pronounced pipe-like pore system with well-aligned macropores.

Effect of mycorrhizae and pH change at the root-soil interface on phosphorus uptake by Sorghum using a rhizocylinder technique

Sorghum (Sorghum bicolor) was grown for 40 days in. rhizocylinder (a growth container which permitted access to rh zosphere and nonrhizosphere soil), in two soils of low P status. Soils were fertilized with different rates of ammonium and nitrate and supplemented with 40 mg phosphorus (P) kg(-1) and inoculated with either Glomus mosseae (Nicol. and Gerd.) or nonmycorrhizal root inoculum.. N-serve (2 mg kg(-1)) was added to prevent nitrification. At harvest, soil from around the roots was collected at distances of 0-5, 5-10, and 10-20 mm from the root core which was 35 mm diameter. Sorghum plants, with and without mycorrhiza, grew larger with NH4+ than with NO3- application. After measuring soil pH, 4 3 suspensions of the same sample were titrated against 0.01 M HCl or 0.01 M NaOH until soil pH reached the nonplanted pH level. The acid or base requirement for each sample was calculated as mmol H+ or OFF kg(-1) soil. The magnitude of liberated acid or base depended on the form and rate of nitrogen and soil type. When the plant root was either uninfected or infected with mycorrhiza., soil pH changes extended up to 5 mm from the root core surface. In both soils, ammonium as an N source resulted in lower soil pH than nitrate. Mycorrhizal (VAM) inoculation did not enhance this difference. In mycorrhizal inoculated soil, P depletion extended tip to 20 mm from the root surface. In non-VAM inoculated soil P depletion extended up to 10 mm from the root surface and remained unchanged at greater distances. In the mycorrhizal inoculated soils, the contribution of the 0-5 mm soil zone to P uptake was greater than the core soil, which reflects the hyphal contribution to P supply. Nitrogen (N) applications that caused acidification increased P uptake because of increased demand; there is no direct evidence that the increased uptake was due to acidity increasing the solubility of P although this may have been a minor effect.

The genome of Rhizobium leguminosarum has recognizable core and accessory components

Background: Rhizobium leguminosarum is an alpha-proteobacterial N-2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841. Results: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes ( Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were overrepresented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens. Conclusion: Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.

Development of a new TDR probe for determining soil water content and dry density

A few traditional methods for determining water content in the field are either inaccurate or time consuming. As an alternative, the time domain reflectometry (TDR) technology has been used in the determination of the soil water content for geotechnical applications. This paper presents the preliminary results on the development of a new TDR probe for determining soil water content and dry density at different depths. This new probe is intended to be pushed into the ground using piezocone equipment. Different from the standard TDR probes with straight rods, the new probe consists of two parallel copper stripes coiled around a PVC-steel core. The probe diameter is the same as the standard 10 cm2 piezocone diameter. Through laboratory calibrations, it is possible to establish expressions relating the soil apparent dielectric constant and the bulk electrical conductivity with the gravimetric water content and the dry density. Copyright ASCE 2007.

Impact of metal and metal oxide engineered nanoparticles in soil and plant systems

Nanotechnology promises huge benefits for society and capital invested in this new technology is steadily increasing, therefore there is a growing number of nanotechnology products on the market and inevitably engineered nanomaterials will be released in the atmosphere with potential risks to humans and environment. This study set out to extend the comprehension of the impact of metal (Ag, Co, Ni) and metal oxide (CeO2, Fe3O4, SnO2, TiO2) nanoparticles (NPs) on one of the most important environmental compartments potentially contaminated by NPs, the soil system, through the use of chemical and biological tools. For this purpose experiments were carried out to simulate realistic environmental conditions of wet and dry deposition of NPs, considering ecologically relevant endpoints. In detail, this thesis involved the study of three model systems and the evaluation of related issues: (i) NPs and bare soil, to assess the influence of NPs on the functions of soil microbial communities; (ii) NPs and plants, to evaluate the chronic toxicity and accumulation of NPs in edible tissues; (iii) NPs and invertebrates, to verify the effects of NPs on earthworms and the damaging of their functionality. The study highlighted that NP toxicity is generally influenced by NP core elements and the impact of NPs on organisms is specie-specific; moreover experiments conducted in media closer to real conditions showed a decrease in toxicity with respect to in vitro test or hydroponic tests. However, only a multidisciplinary approach, involving physical, chemical and biological skills, together with the use of advanced techniques, such as X-ray absorption fine structure spectroscopy, could pave the way to draw the right conclusions and accomplish a deeper comprehension of the effects of NPs on soil and soil inhabitants.

Isotopes Trace Biogeochemistry and Sources of Cu and Zn in an intertidal soil

River floodplain soils are sinks and potential sources for toxic trace metals like Cu and Zn. We hypothesize that stable Cu and Zn isotope ratios reflect both the mobilization and the sources of metals. We determined the soil properties, the concentrations and partitioning of Cu and Zn, and variations in δ65Cu and δ66Zn values in a core obtained from an Aquic Udifluvent developed on a freshwater intertidal mudflat of the River Elbe, Germany. The core was sampled at 2 cm intervals to a depth of 34 cm, which corresponds to approximately 9 yr of sedimentation. Elevated concentrations of Cu (up to 320 μg g−1) and Zn (up to 2080 μg g−1) indicated anthropogenic pollution. At the time of sampling the redox conditions changed from oxic (Eh 200 to 400 mV, above 22 cm deep) to strongly anoxic conditions (-100 to -200 mV, below 22 cm deep). The δ65Cu values varied systematically with depth (from -0.02 to 0.16‰) and were correlated with the Fe, C, and N concentrations. Although pre-depositional variations cannot be ruled out, the systematic variation with depth suggests post-sedimentation fractionation of δ65Cu in response to seasonally variable organic matter deposition and redox conditions. In contrast, the δ66ZnIRMM values were uniform (from -0.07 to 0.01‰) throughout the core, indicating that the Zn isotopes did not significantly fractionate after deposition and that the Zn sources were homogeneous throughout the sedimentation.

A High-Resolution Record of Atmospheric Dust Composition and Variability Since Ad 1650 from a Mount Everest Ice Core

A Mount Everest ice core analyzed at high resolution for major and trace elements (Sr, Cs, Ba, La, Ce, Pr, Nd, Sm, Eu, Tb, Dy, Ho, Er, Tm, Yb, Lu, Bi, U, Tl, Al, S, Ca, Ti, V, Cr, Mn, Fe, Co) and spanning the period A. D. 1650- 2002 is used to investigate the sources of and variations in atmospheric dust through time. The chemical composition of dust varies seasonally, and peak dust concentrations occur during the winter-spring months. Significant correlations between the Everest dust record and dust observations at stations suggest that the Everest record is representative of regional variations in atmospheric dust loading. Back-trajectory analysis in addition to a significant correlation of Everest dust concentrations and the Total Ozone Mapping Spectrometer (TOMS) aerosol index indicates that the dominant winter sources of dust are the Arabian Peninsula, Thar Desert, and northern Sahara. Factors that contribute to dust generation at the surface include soil moisture and temperature, and the long-range transport of dust aerosols appears to be sensitive to the strength of 500-mb zonal winds. There are periods of high dust concentration throughout the 350-yr Mount Everest dust record; however, there is an increase in these periods since the early 1800s. The record was examined for recent increases in dust emissions associated with anthropogenic activities, but no recent dust variations can be conclusively attributed to anthropogenic inputs of dust.

Pollen and macroremains from sediment core Aschenhütte

The Upper Pleistocene sediments of the Aschenhütte sink-hole (west of Herzberg am Harz, Lower Saxony) enable one to make interesting correlations between palynological and geological results. The sequence is composed of limnic-telmatic deposits (Eemain to Lower Weichselian) and loess with paleosoils (Weichselian). Sedimentation started during the hornbeam-dominated phase of the Eemian interglacial period and continued throughout the Eemian, the Weichselian Brörup interstadial (sensu Andersen) and parts of the preceding and the following stadial phases, the Herning and the Rederstall stadials. As opposed to most of the known Eemian sites spruce was a major tree species during the hornbeam-dominated phase of the Eemian. The vegetational development during the interstadial phase does not show a period of climatic deterioration as is the case for the Brörup interstadial when considering regions with a more demanding vegetation or regions close to the natural boundaries of the tree species concerned. Pollen or seeds of Bruckenthalia and Picea omoricoides have not been found in the Aschenhütte cores. The limnic-telmatic sediments interlock with loess-paleosoils (Eemian soil and Lower Weichselian bleaching soils) at the lake shore. They are overlaid by loess paleosoils of the Stillfried-B interstadial (Hattorf soil and Lohne soil). Lake level fluctuations were determined by means of the facies distribution and isochrones as defined by pollen analysis. A relatively high stand of the lake level existed after the end of the Eemian interglacial and during the Brörup interstadial periods. In the course of the Herning stadial period the water level dropped, whereas during the Rederstall stadial phase the lake basin was covered by sediments and therefore dried up.

Geophysical logging on sediment core and hole CRP-3 from the Ross Sea, Antarctica

Cape Roberts drillhole CRP-3 in the northern part of McMurdo Sound (Ross Sea, Antarctica) targeted the western margin of the Victoria Land basin to investigate Neogene to Palaeogene climatic and tectonic history by obtaining continuous core and downhole logs (Cape Roberts Science Team, 2000). The CRP-3 drillhole extended to 939.42 mbsf (meters below seafloor) at a water depth of 297 m. The first downhole measurements after drilling were the temperature and salinity logs. Both were measured at the beginning and at the end of each of the three logging phases. Although an equilibrium temperature state may not have been fully reached after drilling, the temperature and salinity profiles seem to be scarcely disturbed. The average overall temperature gradient calculated from all temperature measurements is 28.5 K/km; remarkably lower than the temperature gradients found in other boreholes in the western Ross See and the Transantarctic Mountains. Anomalies in the salinity profiles at the beginning of each logging phase were no longer present at the end of the corresponding logging phase. This pattern indicates that drilling mud invaded the formation during drilling operations and flowed back into the borehole after drilling ceased. Thus, zones of temperature and salinity anomalies identify permeable zones in the formation and may be pathways for fluid flow. Radiogenic heat production, calculated from the radionuclide contents, is relatively low, with average values between 0.5 and 1.0 pW/m3. The highest values (up to 2 µW/m3) were obtained for the lower part of the Beacon Sandstone below 855 mbsf. The heat flow component due to radiogenic heat production integrated over the entire borehole is 0.7 mW/m2. Thermal conductivities range from 1.3 to 3 W/mK with an average value of 2.1 W/mK over the Tertiary section. Together with the average temperature gradient of 28.5 K/km this yields an average heat flow value of 60 mW/m2.

Magnetic properties, grain sizes, XRF Scanner Data of sediment core GeoB9307-3

Geochemical and mineralogical proxies for paleoenvironmental conditions have the underlying assumption that climate variations have an impact on terrestrial weathering conditions. Varying properties of terrigenous sediments deposited at sea are therefore often interpreted in terms of paleoenvironmental change. Also in gravity core GeoB9307-3 (18° 33.99' S, 37° 22.89' E), located off the Zambezi River, environmental changes during Heinrich Stadial 1 (HS 1) and the Younger Dryas (YD) are accompanied by changing properties of the terrigenous sediment fraction. Our study focuses on the relationship of variability in the hydrological system and changes in the magnetic properties, major element geochemistry and granulometry of the sediments. We propose that changes in bulk sedimentary properties concur with environmental change, although not as a direct response of climate driven pedogenic processes. Spatial varying rainfall intensities on a sub-basin scale modify sediment export from different parts of the Zambezi River basin. During humid phases, such as HS 1 and the YD, sediment was mainly exported from the coastal areas, while during more arid phases sediments mirror the hinterland soil and lithological properties and are likely derived from the northern Shire sub-basin. We propose that a de-coupling of sedimentological and organic signals with variable discharge and erosional activity can occur.

Collection of data on soil carbon (particulate and dissolved) in the Jena Experiment (Main Experiment, time series since 2002)

This data set contains three time series of measurements of soil carbon (particular and dissolved) from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. 1. Particulate soil carbon: Stratified soil sampling was performed every two years since before sowing in April 2002 and was repeated in April 2004, 2006 and 2008 to a depth of 30 cm segmented to a depth resolution of 5 cm giving six depth subsamples per core. Total carbon concentration was analyzed on ball-milled subsamples by an elemental analyzer at 1150°C. Inorganic carbon concentration was measured by elemental analysis at 1150°C after removal of organic carbon for 16 h at 450°C in a muffle furnace. Organic carbon concentration was calculated as the difference between both measurements of total and inorganic carbon. 2. Particulate soil carbon (high intensity sampling): In one block of the Jena Experiment soil samples were taken to a depth of 1 m (segmented to a depth resolution of 5 cm giving 20 depth subsamples per core) with three replicates per block ever 5 years starting before sowing in April 2002. Samples were processed as for the more frequent sampling. 3. Dissolved organic carbon: Suction plates installed on the field site in 10, 20, 30 and 60 cm depth were used to sample soil pore water. Cumulative soil solution was sampled biweekly and analyzed for dissolved organic carbon concentration by a high TOC elemental analyzer. Annual mean values of DOC are provided.

Amino acid data of catchment and sediment core samples of four Indian lakes

In the present study, we report the results of comprehensive amino acid (AA) analyses of four Indian lakes from different climate regimes. We focus on the investigation of sediment cores retrieved from the lakes but data of modern sediment as well as vascular plant, soil, and suspended particulate matter samples from individual lakes are also presented. Commonly used degradation and organic matter source indices are tested for their applicability to the lake sediments, and we discuss potential reasons for possible limitations. A principal component analysis including the monomeric AA composition of organic matter of all analysed samples indicates that differences in organic matter sources and the environmental properties of the individual lakes are responsible for the major variability in monomeric AA distribution of the different samples. However, the PCA also gives a factor that most probably separates the samples according to their state of organic matter degradation. Using the factor loadings of the individual AA monomers, we calculate a lake sediment degradation index (LI) that might be applicable to other palaeo-lake investigations.