Do Botanical Pesticides Alter the Structure of the Soil Microbial Community?

The effects of synthetic pesticides on the soil microbial community have been thoroughly investigated in the past mostly by culture-dependent methods and only few recent studies have used culture-independent approaches for this purpose. However, it should be noted that most of these studies have been conducted in microcosms where the soil microbial community is exposed to unrealistic concentrations of the pesticides, providing an unrealistic exposure scheme for soil microorganism. On the other hand, little is known regarding the potential impact of botanical pesticides on the soil microbial community. Therefore, a laboratory study and a field study were conducted to investigate the effects of synthetic (metham sodium [MS], sodium tetrathiocarbonate [SoTe], and fosthiazate) and botanical pesticides (azadirachtin, quillaja, and pulverized Melia azedarach fruits [PMF]) on the soil microbial community using phospholipid fatty acids (PLFA) analysis. Principal component analysis (PCA) on the results of the laboratory study indicated that the application of PMF resulted in significant changes in the soil microbial community. This was obvious by the proportional increase in the abundance of fatty acids 18:1ω9cis, 18:1ω9trans, which are common in gram-negative bacteria and saprotrophic fungi, and 18:2ω6,9, which is a fungal indicator. This response was attributed to the release of copious amounts of organic carbon and nutrients in the soil by the PMF. On the other hand, MS inhibited fungi and gram-negative bacteria, while fosthiazate and the botanical pesticides quillaja and azadirachtin did not impose significant changes in the soil microbial community. Similar results were obtained by the field study where application of the fumigants MS and SoTe significantly altered the structure of the soil microbial community with the former having a more prominent effect. Fosthiazate imposed mild changes in the soil microbial community, whereas quillaja and azadirachtin again did not show a significant effect. Overall, botanical pesticides, at their recommended dose, did not alter the structure of the soil microbial community compared to synthetic nonfumigant and fumigant pesticides which induced significant changes.     

Three-dimensional Microorganization of the Soil–Root–Microbe System

Soils contain the greatest reservoir of biodiversity on Earth, and the functionality of the soil ecosystem sustains the rest of the terrestrial biosphere. This functionality results from complex interactions between biological and physical processes that are strongly modulated by the soil physical structure. Using a novel combination of biochemical and biophysical indicators and synchrotron microtomography, we have discovered that soil microbes and plant roots microengineer their habitats by changing the porosity and clustering properties (i.e., spatial correlation) of the soil pores. Our results indicate that biota act to significantly alter their habitat toward a more porous, ordered, and aggregated structure that has important consequences for functional properties, including transport processes. These observations support the hypothesis that the soil–plant–microbe complex is self-organized.     

Co-Composting of Soil Heavily Contaminated with Creosote with Cattle Manure and Vegetable Waste for the Bioremediation of Creosote–Contaminated Soil

Mispah form (FAO: Lithosol) soil contaminated with >380 000 mg kg^?1 creosote was co-composted with cattle manure and mixed vegetable waste for 19 months. The soil was mixed with wood chips to improve aeration and then mixed with cattle manure or mixed vegetable waste in a ratio of 4:1. Moisture, temperature, pH, ash content, C:N ratios, and the concentrations of creosote in the compost systems were monitored monthly. The concentrations of selected hydrocarbons in the compost systems were determined at the end of composting. Temperature rose to about 45°C in the cattle manure compost within two months of incubation while temperature in the control and vegetable waste remained below 30°C until the fourth month. Creosote concentration was reduced by 17% in the control and by more than 99% in the cattle manure and vegetable waste compost after composting. The rate of reduction in concentration in the mixed vegetable waste compost was initially lower than in the cattle manure compost. The reduction rate became similar in later months with only small differences towards the end of the composting. The concentrations of selected creosote components were reduced by between 96% and 100% after composting. There was no significant difference in reduction in concentration in both compost systems at p 0.05. Microbial activity correlated with reduction in creosote concentration.     

Mathematical Modeling of the Dynamics of Plant Mineral Nutrition in the Fertilizer–Soil–Plant System

A numerical simulation of the spatial–temporal dynamics of a multi-parameter system has been developed. The components of this system are plant biomass, the mobile and stationary forms of mineral nutrition elements, rhizosphere microorganisms, and environmental parameters (temperature, humidity, and acidity). Parametric identification and verification of the adequacy of the model were carried out based on the experimental data on the growth of Krasnoufimskaya-100 spring wheat on peat lowland soil. The results are represented by temporal distributions of biomass from agricultural crops and the findings on the contents of the main nutrition elements within the plant (nitrogen, phosphorus, and potassium). An agronomic assessment and interpretation of the results are given.

     

Soil temperatures after the passage of a fire: Do they influence the germination of buried seeds?

Abstract Soil temperatures down to a depth of 5 cm were measured in the days following one fire in summer, one fire in winter and in unburnt vegetation during summer. Soil temperatures did not rise above 40°C after the winter fire or in unburnt vegetation during summer. Consequently, no impact on seed dormancy in the soil seedbank was expected. After a summer fire, soil temperatures above 40°C were found up to 4.5 cm in depth, while temperatures above 60°C were found only in the top 0.5 cm of soil. These temperatures are sufficient to break seed dormancy in some legume species in the seedbank. Hence, the season of burn may influence the number of seeds in the soil that have their dormancy broken and subsequent germination levels.     

Impacts of Environmental Colloids on the Transport of 17 β-estradiol in Intact Soil Cores

Estrogens such as 17-β estradiol (E2) are endocrine-disrupting compounds and can affect the reproductive systems of aquatic organisms. Therefore, it is important to understand the mechanisms of their transport in the environment. E2 and its daughter product estrone (E1) are both strongly adsorbed by soil organic matter and have relatively short half-lives. Reduced contact time with soil makes transport of E2 and E1 in soil more likely. In this study, intact soil cores from three soils representing a range of particle size distribution, structure, and organic matter content were used to compare the transport of E2 with and without the presence of colloidal material fractionated from soil or swine manure. In chemical transport experiments conducted with undisturbed soil columns, E2 and E1 were measured both in solution and attached to suspended solids in column effluent. During the transport experiments, colloids carrying E2 passed through all soils, with the exception of the sandy soil. The presence of colloids decreased the first detection time of E2 in the aqueous phase, was correlated with greater peak E2 concentrations in the effluent of both loamy and clayey soils, but not through the sandy soil, and increased mass fractions of the E2 that was transported.     

Predicting Soil Salinity with Vis–NIR Spectra after Removing the Effects of Soil Moisture Using External Parameter Orthogonalization

Robust models for predicting soil salinity that use visible and near-infrared (vis–NIR) reflectance spectroscopy are needed to better quantify soil salinity in agricultural fields. Currently available models are not sufficiently robust for variable soil moisture contents. Thus, we used external parameter orthogonalization (EPO), which effectively projects spectra onto the subspace orthogonal to unwanted variation, to remove the variations caused by an external factor, e.g., the influences of soil moisture on spectral reflectance. In this study, 570 spectra between 380 and 2400 nm were obtained from soils with various soil moisture contents and salt concentrations in the laboratory; 3 soil types × 10 salt concentrations × 19 soil moisture levels were used. To examine the effectiveness of EPO, we compared the partial least squares regression (PLSR) results established from spectra with and without EPO correction. The EPO method effectively removed the effects of moisture, and the accuracy and robustness of the soil salt contents (SSCs) prediction model, which was built using the EPO-corrected spectra under various soil moisture conditions, were significantly improved relative to the spectra without EPO correction. This study contributes to the removal of soil moisture effects from soil salinity estimations when using vis–NIR reflectance spectroscopy and can assist others in quantifying soil salinity in the future.     

The Effect of γ-Radiation and Desiccation on the Viability of the Soil Bacteria Isolated from the Alienated Zone around the Chernobyl Nuclear Power Plant

Methylobacterium extorquens, M. mesophilicum, and Bacillus subtilis strains were found to be resistant to -radiation, irrespective of whether they were isolated from the alienated zone around the Chernobyl Nuclear Power Plant or outside this zone. The LD₉₀ of Methylobacterium and B. subtilis strains with respect to -radiation was 2.0–3.4 and 3.7–4.4 kGy, respectively, whereas their LD_99.99 values were 4.5–6.9 and more than 10 kGy, respectively. The high threshold levels of -radiation for Methylobacterium and B. subtilis imply the efficient functioning of DNA repair systems in these bacteria. Unlike Bacillus polymyxa cells, the cells of M. extorquens, M. mesophilicum, and B. subtilis were also resistant to desiccation. Pseudomonas sp., Nocardiasp., and nocardioform actinomycetes were sensitive to both -radiation and desiccation. Similar results were obtained when the bacteria studied were exposed to hydrogen peroxide and ultraviolet radiation. The results obtained indicate that the bacteria that are resistant to -radiation are also resistant to desiccation, UV radiation, and hydrogen peroxide. The possibility of using common laboratory tests (such as the determination of bacterial resistance to UV light and desiccation) for the evaluation of bacterial resistance to -radiation is discussed.     

Common Physical Errors in the Description of Water Fluxes in the Soil–Plant–Atmosphere System

Widely accepted concepts and definitions concerning the driving forces of upward water fluxes, such as osmotic pressure (OP) and water potential (WP), were analyzed in the soil–plant–atmosphere system. It is emphasized that, at present, there are no physically correct definitions of the mentioned parameters, because such a concept as the heat pressure of molecules in a liquid has not been introduced. Physical definitions of OP and WP are presented. It is demonstrated that WP is not a driving force for water fluxes at the water–vapor interface. The fundamental difference in mechanisms of diffusion fluxes and active transport across the biological membranes is analyzed. The biological specificity of driving forces at the soil–root and leaf–air interfaces is described.     

Microevolution of Nodule Bacteria upon Generation of Mutants with Altered Survival in the Plant–Soil System

Simulation of cyclic processes in the plant–soil system was used to analyze the effects of factors responsible for the population dynamics of rhizobia on generation of mutants with changedex planta viability. Rhizobial evolution in a system of ecological niches (soil, rhizosphere, nodules) was described with recurrent equations. Computer experiments were carried out with parameters determining the mutation pressure, selection, and amplitude of the population wave arising in soil on the release of bacteria from nodules and the rhizosphere. Analysis of the model showed that (1) mutants with enhanced ex planta viability do not completely replace the parental strain and (2) mutants with impaired ex planta viability may be fixed in the population. The maintenance of genotypes subject to elimination from the soil and rhizosphere by Darwinian selection was associated with frequency-dependent selection (FDS), which is effective in competition for nodulation. The FDS index was proposed to characterize FDS pressure and was shown to determine the population polymorphism for adaptive traits. An increase in population wave amplitude proved to increase the fixation level (the proportion in the limiting state of the system) of mutants with enhanced viability and to decrease it in mutants with low viability. The results obtained with the model agreed with the data that, in edaphic stress, rhizobial populations remain highly polymorphic, which is associated with the maintenance of sensitive strains. The simulation procedure may be employed in estimating the genetic consequences of introduction of modified rhizobial strains in the environment.     

Plant–Soil Feedbacks Contribute to the Persistence of Bromus inermis in Tallgrass Prairie

As invasive plants become a greater threat to native ecosystems, we need to improve our understanding of the factors underlying their success and persistence. Over the past 30 years, the C₃ nonnative plant Bromus inermis (smooth brome) has been spreading throughout the central grasslands in North America. Invasion by this grass has resulted in the local displacement of natives, including the tallgrass species Panicum virgatum (switchgrass). To determine if factors related to resource availability and plant–soil interactions were conferring a competitive advantage on smooth brome, field plots were set up under varying nitrogen (N) levels. Plots composed of a 1:1 ratio of smooth brome and switchgrass were located in a restored tallgrass prairie and were randomly assigned one of the following three N levels: (a) NH₄NO₃ added to increase available N, (b) sucrose added to reduce available N, and (c) no additions to serve as control. In addition, soil N status, soil respiration rates, plant growth, and litter decomposition rates were monitored. Results indicate that by the 2nd year, the addition of sucrose significantly reduced available soil N and additions of NH₄NO₃ increased it. Further, smooth brome had greater tiller density, mass, and canopy interception of light on N-enriched soils, whereas none of these characteristics were stimulated by added N in the case of switchgrass. This suggests that smooth brome may have a competitive advantage on higher-N soils. Smooth-brome plant tissue also had a lower carbon–nitrogen (C:N) ratio and a higher decomposition rate than switchgrass and thus may cycle N more rapidly in the plant–soil system. These differences suggest a possible mechanism for the persistence of smooth brome in the tallgrass prairie: Efficient recycling of nutrient-rich litter under patches of smooth brome may confer a competitive advantage that enables it to persist in remnant or restored prairies. Increased N deposition associated with human activity and changing land use may play a critical role in the persistence of smooth brome and other N-philic exotic species.     

Can the Study of Natural Vegetation Succession Assist in the Control of Soil Erosion on Abandoned Croplands on the Loess Plateau,China?

In the Loess Plateau, China, arable cultivation of slope lands is common and associated with serious soil erosion. Planting trees or grass may control erosion, but planted species may consume more soil water and can threaten long‐term ecosystem sustainability. Natural vegetation succession is an alternative ecological solution to restore degraded land, but there is a time cost, given that the establishment of natural vegetation, adequate to prevent soil erosion, is a longer process than planting. The aims of this study were to identify the environmental factors controlling the type of vegetation established on abandoned cropland and to identify candidate species that might be sown soon after abandonment to accelerate vegetation succession and establishment of natural vegetation to prevent soil erosion. A field survey of thirty‐three 2 × 2–m plots was carried out in July 2003, recording age since abandonment, vegetation cover, and frequency of species together with major environmental and soil variables. Data were analyzed using correspondence analysis, classification tree analysis, and species response curves. Four vegetation types were identified and the data analysis confirmed the importance of time since abandonment, total P, and soil water in controlling the type of vegetation established. Among the dominant species in the three late‐successional vegetation types, the most appropriate candidates for accelerating and directing vegetation succession were King Ranch bluestem (Bothriochloa ischaemum) and Lespedeza davurica (Leguminosae). These species possess combinations of the following characteristics: tolerance of low water and nutrient availability, fibrous root system and strong lateral vegetative spread, and a persistent seed bank.     

Soil Microbial Diversity in the Vicinity of a Negev Desert Shrub��Reaumuria negevensis

The Negev Desert is characterized by low soil-water availability and organic matter content, as well as important factors significantly influencing soil biological activity. In order to overcome the xeric environment, plant and soil biota have evolutionarily developed, over time, ecophysiological abilities that help them fulfill their biological role and function. Microorganisms are known as a major part of the ecosystem's total biomass and play an important role in decomposition processes and the nutrient cycle. Perennial shrubs have been found to play an important role as organic matter suppliers and as a physical barrier prolonging biological activity of microbial communities. Soil samples were collected monthly, from November 2006 to November 2007, from a 0 to 10-cm depth under the canopies of Reaumuria negevensis and from open areas (control) in order to evaluate abiotic components and microbial variables on a temporal basis. H' values, evenness, and β diversity (S?rensen's similarity) were determined by a molecular method based on sequencing. Water availability, organic matter content, and total soluble nitrogen were higher in soil samples collected in the vicinity of R. negevensis than in samples collected in open areas. Our study also indicated that, in spite of the similarity between H' values of soil samples collected in the vicinity of R. negevensis and the open area, a low percentage of similarity was found between the soil bacterial populations. These results support the hypothesis that distribution of resources in the environment under R. negevensis shrubs varies in space and time and also influences soil microbial diversity and the abiotic environmental role.     

Soil fertility alters the nature of plant–resource interactions in invaded grassland communities

Resource competition theory suggests that the nature of diversity–resource–invasibility interactions will vary along fertility gradients, concurrent with changes in the relative availability of limiting above- versus below-ground resources. Experimental support for this contingency is lacking. Here, we manipulated resident diversity, baseline fertility, and the availabilities of light and soil nitrogen in grassland communities invaded by two functionally distinct non-native plant species (Lolium arundinaceum and Melilotus alba). We tested the hypotheses that increased resident diversity reduces community invasibility and dampens the effects of light and soil nitrogen pulses, and that the relative effects of light versus soil nitrogen additions on diversity–invasibility relationships depend on the baseline fertility of the study system. Our results reveal an overall weak negative effect of resident diversity on Lolium performance, but in contrast to our expectations, this diversity effect did not vary with light or soil nitrogen additions or with baseline fertility. However, the relative effects of above- versus below-ground resource additions on invader performance varied with baseline fertility as expected: Lolium responded most strongly to soil nitrogen additions in low-fertility mesocosms and most strongly to increased light availability in high-fertility mesocosms. In contrast to Lolium, nitrogen-fixing Melilotus was overall less responsive to diversity and resource manipulations. Together, these patterns do not lend support for the dependence of diversity–resource–invasibility relationships on either baseline fertility or invasive species identity, but they do highlight the dominant role of resources over diversity in determining invader performance, as well as the manner in which fertility alters the relative importance of above- versus below-ground resource pulses in promoting invasions.     

Degradation of the Herbicide Atrazine by the Soil Mycelial Fungus INBI 2-26 (–), a Producer of Cellobiose Dehydrogenase

Nonsporulating mycelial fungi producing cellobiose dehydrogenase (CDH) and isolated from soils of South Vietnam with a high residual content of dioxins are capable of growing on a solid medium in the presence of high atrazine concentrations (to 500 mg/l). At 20 and 50 mg/l atrazine, the area of fungal colonies was 1.5–1.2-fold larger, respectively, than the control colonies of the same age, whereas development of the colonies at 500 mg/l atrazine was delayed by 5 days, compared with controls grown in the absence of atrazine. Surface cultivation of the fungus on a minimal medium with glucose as a sole source of carbon and energy decreased the initial concentration of atrazine (20 mg/l) 50 times in 40 days; in addition, no pronounced sorption of atrazine by mycelium was detected. This was paralleled by an accumulation in the culture medium of extracellular CDH; atrazine increased the synthesis of this enzyme two- to threefold. Accumulation of -glucosidase (a mycelium-associated enzyme) and cellulases preceded the formation of CDH.     

What's in a beach? Soil micromorphology of sediments from the Lower Paleolithic site of 'Ubeidiya, Israel

A micromorphological study of archaeological sediments from the early Pleistocene site of 'Ubeidiya (Jordan Valley, Israel) was conducted to provide microenvironmental detail for the hominin occupation contexts and investigate site formation issues. Previous research shows that the hominin groups occupied the marshes and pebbly beaches at the shores of a lake during a regressive period, but given that some portions of the lithic and faunal assemblages are abraded and others fresh, there remains a question of whether the archaeological assemblages are in situ or reworked, and if reworked, by what mechanisms and from where. The rates of sedimentation within the regressive cycle, by which we can learn about the frequency and duration of exposed surfaces amenable for hominin occupation is also unknown. Finally, the artificial nature of some of the pebbly layers has been questioned. The micromorphological analysis yielded the identification of twelve microfacies; the majority of these represent fluvially derived floodplain soils or distal mudflow deposits, and a minor number are sediments of lacustrine origin: mudflats and shallow subaqueous sediments. These represent the natural habitats of the 'Ubeidiya hominins and might serve as a reference to similar contexts of other early hominin sites. The sedimentary model proposed here entails the rapid deposition of fluvially derived low-energy sediments at and around the shoreline, followed by prolonged periods of exposure, during which surfaces stabilized within a relatively wet, marshy environment. This interpretation suggests that the abraded portions of the archaeological assemblages are a result of prolonged surface exposure rather than high-energy transport from a distant source or to wave reworking at the shoreline, and supports the consideration of these assemblages as archaeological palimpsests, with locally reworked fresh and abraded elements. No micromorphological evidence supporting anthropogenic agency in the formation of the pebbly layers was found. The entire regressive cycle entailed unvarying climatic conditions with seasonal fluctuations and episodic lacustrine incursions, and with a trend towards arid conditions in the end.     

Soil�Cstrain compatibility: the key to effective use of arbuscular mycorrhizal inoculants?

Consistency of response to arbuscular mycorrhizal (AM) inoculation is required for efficient use of AM fungi in plant production. Here, we found that the response triggered in plants by an AM strain depends on the properties of the soil where it is introduced. Two data sets from 130 different experiments assessing the outcome of a total of 548 replicated single inoculation trials conducted either in soils with a history of (1) high input agriculture (HIA; 343 replicated trials) or (2) in more pristine soils from coffee plantations (CA; 205 replicated trials) were examined. Plant response to inoculation with different AM strains in CA soils planted with coffee was related to soil properties associated with soil types. The strains Glomus fasciculatum-like and Glomus etunicatum-like were particularly performant in soil relatively rich in nutrients and organic matter. Paraglomus occultum and Glomus mosseae-like performed best in relatively poor soils, and G. mosseae and Glomus manihotis did best in soils of medium fertility. Acaulospora scrobiculata, Diversispora spurca, G. mosseae-like, G. mosseae and P. occultum stimulated coffee growth best in Chromic, Eutric Alluvial Cambisol, G. fasciculatum-like and G. etunicatum-like in Calcaric Cambisol and G. manihotis, in Chromic, Eutric Cambisols. Acaulospora scrobiculata and Diversispora spurca strains performed best in Chromic Alisols and Rodic Ferralsols. There was no significant relationship between plant response to AM fungal strains and soil properties in the HIA soil data set, may be due to variation induced by the use of different host plant species and to modification of soil properties by a history of intensive production. Consideration of the performance of AM fungal strains in target soil environments may well be the key for efficient management of the AM symbiosis in plant production.     

Biogenic Catalysis of Soil Formation on Mars?

The high iron abundance and the weak ferric iron spectral features of martian surface material are consistent with nanophase (nm-sized) iron oxide minerals as a major source of iron in the bright region soil on Mars. Nanophase iron oxide minerals, such as ferrihydrite and schwertmannite, and nanophase forms of hematite and goethite are formed by both biotic and abiotic processes on Earth. The presence of these minerals on Mars does not indicate biological activity on Mars, but it does raise the possibility. This work includes speculation regarding the possibility of biogenic soils on Mars based on previous observations and analyses. A remote sensing goal of upcoming missions should be to determine if nanophase iron oxide minerals, clay silicates and carbonates are present in the martian surface material. These minerals are important indicators for exobiology and their presence on Mars would invoke a need for further investigation and sample return from these sites.     

Response of Soil Bacterial Community Structure to Permafrost Degradation in the Upstream Regions of the Shule River Basin,Qinghai–Tibet Plateau

Permafrost degradation affects soil properties and vegetation, but little is known about its consequent effects on the soil bacterial community. In this study, we analyzed the bacterial community structure of 12 permafrost-affected soil samples from four principal permafrost types, sub-stable permafrost (SSP), transition permafrost (TP), unstable permafrost (UP) and extremely unstable permafrost (EUP), to investigate the effects of vegetation characteristics and soil properties on bacterial community structure during the process of permafrost degradation. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the predominant phyla in all four permafrost soil types. The relative abundance of Proteobacteria decreased in the order SSP > TP> UP > EUP, whereas the abundance of Actinobacteria increased in the order SSP < TP < UP < EUP. Moreover, the Actinobacteria/Proteobacteria ratio increased significantly in the order SSP < TP < UP < EUP along with permafrost degradation, which may be useful as a sign of permafrost degradation. Redundancy analysis (RDA) showed that bacterial communities could be clustered by permafrost types. Analysis of single factors revealed that soil moisture (SM) was the most important factor affecting the bacterial community structure and diversity, followed by soil total nitrogen (STN) and vegetation cover (VC). Partial RDA analysis showed that the soil properties and vegetation characteristics jointly shaped the bacterial community structure. Hence, we can conclude that permafrost degradation, caused by global warming, affects vegetation and soil properties and consequently drives changes in the soil bacterial community structure.     

Long-distance ABA Signaling and Its Relation to Other Signaling Pathways in the Detection of Soil Drying and the Mediation of the Plant’s Response to Drought

In this article we review evidence for a variety of long-distance signaling pathways involving hormones and nutrient ions moving in the xylem sap. We argue that ABA has a central role to play, at least in root-to-shoot drought stress signaling and the regulation of functioning, growth, and development of plants in drying soil. We also stress the importance of changes in the pH of the leaf cell apoplast as influenced both by edaphic and climatic variation, as a regulator of shoot growth and functioning, and we show how changes in xylem and apoplastic pH can affect the way in which ABA regulates stomatal behavior and growth. The sensitivity to drought of the pH/ABA sensing and signaling mechanism is emphasized. This allows regulation of plant growth, development and functioning, and particularly shoot water status, as distinct from stress lesions in growth and other processes as a reaction to perturbations such as soil drying.