Assessment of toxicological interactions of benzene and its primary degradation products (catechol and phenol) using a lux-modified bacterial bioassay

A bacterial bioassay has been developed to assess the relative toxicities of xenobiotics commonly found in contaminated soils, rivers, waters, and ground waters. The assay utilized decline in luminescence of lux- marked Pseudomonas fluorescens on exposure to xenobiotics. Pseudomonas fluorescens is a common bacterium in the terrestrial environment, providing environmental relevance to soil, river, and ground water systems. Three principal environmental contaminants associated with benzene degradation were exposed to the luminescence-marked bacterial biosensor to assess their toxicity individually and in combination. Median effective concentration (EC50) values for decline in luminescence were determined for benzene, catechol, and phenol and were found to be 39.9, 0.77, and 458.6 mg/L, respectively. Catechol, a fungal and bacterial metabolite of benzene, was found to be significantly more toxic to the biosensor than was the parent compound benzene, showing that products of xenobiotic biodegradation may be more toxic than the parent compounds. Combinations of parent compounds and metabolites were found to be significantly more toxic to the bioassay than were the individual compounds themselves. Development of this bioassay has provided a rapid screening system suitable for assessing the toxicity of xenobiotics commonly found in contaminated soil, river, and ground-water environments. The assay can be utilized over a wide pH range and is therefore more applicable to such environmental systems than bioluminescence-based bioassays that utilize marine organisms and can only be applied over a limited pH and salinity range.

Bioavailability of atrazine to soil microbes in the presence of the earthworm Lumbricus terrestrius (L.)

Experiments were conducted to investigate the interactions between an earthworm species (Lumbricus terrestrius) and soil microflora with respect to the bioavailability and mineralisation of ¹⁴C ring-labelled atrazine. Presence of earthworms had no affect on atrazine in soil solution (assayed by soil centrifugation). This soil solution pool was highly time dependent, decreasing considerably as the experiment proceeded. KCl-extractable label was, however, affected by the presence of earthworms, with this pool initially increasing in the presence of the worms. This pool was also highly time-dependent although, the pattern of this dependence did not follow that for label in soil solution. Mineralisation of the atrazine closely followed the KCl exchangeable pool and not that of the soil solution pool. However, label sorbed to the surface of the worms was closely correlated to the soil solution pool. Mineralisation in the presence of earthworms was double that of the controls. By the end of the experiment 6% of added radioactivity was present in the earthworm biomass.

Combined effects of chemical and natural stressors to soil organisms and plants

Nas últimas décadas, a Terra tem experimentado um aquecimento global e mudanças nos padrões de precipitação. Muitos estudos sobre a avaliação de risco de agrotóxicos em organismos não-alvo foram realizados com base em protocolos padronizados, com condições abióticas controladas. Mas, em campo, os organismos são expostos a flutuações de vários fatores ambientais, bem como a poluentes, que podem alterar os limites de tolerância dos organismos aos stressores naturais, bem como alterar a toxicidade ou biodisponibilidade do químico em causa. Considerando isso, o principal objetivo deste trabalho foi o de avaliar de que modo e em que medida os fatores ambientais (temperatura, humidade do solo e radiação UV) podem interagir uns com os outros ou afetar a toxicidade do carbaril para invertebrados do solo e plantas. Para isso, foram utilizadas quatro espécies padrão: Folsomia candida, Eisenia andrei, Triticum aestivum e Brassica rapa, e simulados diferentes cenários climáticos, com vários parâmetros letais e subletais analisados. A exposição combinada foi analisada utilizando, quando possível, a ferramenta MIXTOX, com base no modelo de referência de acção independente (IA) e possíveis desvios, assim como rácios sinergísticos/antagonísticos (a partir de valores de EC50/LC50), quando a dose-resposta de um dos stressores não foi obtida. Todos os fatores de stress aplicados isoladamente causaram efeitos significativos sobre as espécies testadas e sua exposição combinada com carbaril, apresentaram respostas diferenciadas: para as minhocas, a seca e temperaturas elevadas aumentaram os efeitos deletérios do carbaril (sinergismo), enquanto o alagamento e temperaturas baixas diminuíram sua toxicidade (antagonismo). Para os colêmbolos, o modelo IA mostrou ser uma boa ferramenta para prever a toxicidade do carbaril tanto para temperaturas altas como para as baixas. Para as duas espécies de plantas foram encontradas diferenças significativas entre elas: em termos gerais, as interações entre carbaril e os stressores naturais foram observadas, com sinergismo aparecendo como o padrão principal relacionado com a radiação UV, solos secos e temperaturas elevadas, enquanto o padrão principal relacionado com temperaturas baixas e stress de alagamento foi o antagonismo. Quando os efeitos de dois stressores naturais (radiação UV e humidade do solo) em plantas foram avaliados, uma interação significativa foi encontrada: a seca aliviou o efeito deletério da radiação UV em T. aestivum e o alagamento aumentou os seus efeitos, mas para B. rapa a adição de ambos os stresses de água causou um aumento (sinergismo) dos efeitos deletérios da radiação UV para todos os parâmetros avaliados. Portanto é necessário que as diferenças sazonais e latitudinais, bem como as mudanças climáticas globais, sejam integradas na avaliação de risco de contaminantes do solo.

Significance of soil microorganisms with special reference to climate change

There are a large number of agronomic-ecological interactions that occur in a world with increasing levels of CO2, higher temperatures and a more variable climate. Climate change and the associated severe problems will alter soil microbial populations and diversity. Soils supply many atmospheric green house gases by performing as sources or sinks. The most important of these gases include CH4, CO2 and N2O. Most of the green house gases production and consumption processes in soil are probably due to microorganisms. There is strong inquisitiveness to store carbon (C) in soils to balance global climate change. Microorganisms are vital to C sequestration by mediating putrefaction and controlling the paneling of plant residue-C between CO2 respiration losses or storage in semi-permanent soil-C pools. Microbial population groups and utility can be manipulated or distorted in the course of disturbance and C inputs to either support or edge the retention of C. Fungi play a significant role in decomposition and appear to produce organic matter that is more recalcitrant and favor long-term C storage and thus are key functional group to focus on in developing C sequestration systems. Plant residue chemistry can influence microbial communities and C loss or flow into soil C pools. Therefore, as research takings to maximize C sequestration for agricultural and forest ecosystems - moreover plant biomass production, similar studies should be conducted on microbial communities that considers the environmental situations

Alley cropping of willows and grassland for bioenergy provision: productivity, tree-crop interactions and energy balance

The demand for biomass for bioenergy has increased rapidly in industrialized countries in the recent years. Biogenic energy carriers are known to reduce CO2 emissions. However, the resource-inefficient production of biomass often caused negative impacts on the environment, e.g. biodiversity losses, nitrate leaching, and erosion. The detrimental effects evolved mainly from annual crops. Therefore, the aim of modern bioenergy cropping systems is to combine yield stability and environmental benefits by the establishment of mixed-cropping systems. A particular emphasis is on perennial crops which are perceived as environmentally superior to annual crops. Agroforestry systems represent such mixed perennial cropping systems and consist of a mix of trees and arable crops or grassland within the same area of land. Agroforestry practices vary across the globe and alley cropping is a type of agroforestry system which is well adapted to the temperate zone, with a high degree of mechanization. Trees are planted in rows and crops are planted in the alleyways, which facilitates their management by machinery. This study was conducted to examine a young alley cropping system of willows and two grassland mixtures for bioenergy provision under temperate climate conditions. The first part of the thesis identified possible competition effects between willows and the two grassland mixtures. Since light seemed to be the factor most affecting the yield performance of the understory in temperate agroforestry systems, a biennial in situ artificial shade experiment was established over a separate clover-grass stand to quantify the effects of shade. Data to possible below- and aboveground interactions among willows and the two grassland mixtures and their effects on productivity, sward composition, and quality were monitored along a tree-grassland interface within the alleys. In the second part, productivity of the alley cropping system was examined on a triennial time frame and compared to separate grassland and willow stands as controls. Three different conversion technologies (combustion of hay, integrated generation of solid fuel and biogas from biomass, whole crop digestion) were applied to grassland biomass as feedstock and analyzed for its energetic potential. The energetic potential of willow wood chips was calculated by applying combustion as conversion technique. Net energy balances of separate grassland stands, agroforestry and pure willow stands evaluated their energy efficiency. Results of the biennial artificial shade experiment showed that severe shade (80 % light reduction) halved grassland productivity on average compared to a non-shaded control. White clover as heliophilous plant responded sensitively to limited radiation and its dry matter contribution in the sward decreased with increasing shade, whereas non-leguminous forbs (mainly segetal species) benefited. Changes in nutritive quality could not be confirmed by this experiment. Through the study on interactions within the alleys of the young agroforestry system it was possible to outline changes of incident light, soil temperature and sward composition of clover-grass along the tree-grassland interface. Nearly no effects of trees on precipitation, soil moisture and understory productivity occurred along the interface during the biennial experiment. Considering the results of the productivity and the net energy yield alley cropping system had lower than pure grassland stands, irrespective of the grassland seed mixture or fertilization, but was higher than that for pure willow stands. The comparison of three different energetic conversion techniques for the grassland biomass showed highest net energy yields for hay combustion, whereas the integrated generation of solid fuel and biogas from biomass (IFBB) and whole crop digestion performed similarly. However, due to the low fuel quality of hay, its direct combustion cannot be recommended as a viable conversion technique, whereas IFBB fuels were of a similar quality to wood chip from willow.

Predicted soil organic carbon stocks and changes in the Brazilian Amazon between 2000 and 2030

Currently we have little understanding of the impacts of land use change on soil C stocks in the Brazilian Amazon. Such information is needed to determine impacts'6n the global C cycle and the sustainability of agricultural systems that are replacing native forest. The aim of this study was to predict soil carbon stocks and changes in the Brazilian Amazon during the period between 2000 and 2030, using the GEFSOC soil carbon (C) modelling system. In order to do so, we devised current and future land use scenarios for the Brazilian Amazon, taking into account: (i) deforestation, rates from the past three decades, (ii) census data on land use from 1940 to 2000, including the expansion and intensification of agriculture in the region, (iii) available information on management practices, primarily related to well managed pasture versus degraded pasture and conventional systems versus no-tillage systems for soybean (Glycine max) and (iv) FAO predictions on agricultural land use and land use changes for the years 2015 and 2030. The land use scenarios were integrated with spatially explicit soils data (SOTER database), climate, potential natural vegetation and land management units using the recently developed GEFSOC soil C modelling system. Results are presented in map, table and graph form for the entire Brazilian Amazon for the current situation (1990 and 2000) and the future (2015 and 2030). Results include soil organic C (SOC) stocks and SOC stock change rates estimated by three methods: (i) the Century ecosystem model, (ii) the Rothamsted C model and (iii) the intergovernmental panel on climate change (IPCC) method for assessing soil C at regional scale. In addition, we show estimated values of above and belowground biomass for native vegetation, pasture and soybean. The results on regional SOC stocks compare reasonably well with those based on mapping approaches. The GEFSOC system provided a means of efficiently handling complex interactions among biotic-edapho-climatic conditions (> 363,000 combinations) in a very large area (similar to 500 Mha) such as the Brazilian Amazon. All of the methods used showed a decline in SOC stock for the period studied; Century and RothC simulated values for 2030 being about 7% lower than those in 1990. Values from Century and RothC (30,430 and 25,000 Tg for the 0-20 cm layer for the Brazilian Amazon region were higher than those obtained from the IPCC system (23,400 Tg in the 0-30 cm layer). Finally; our results can help understand the major biogeochemical cycles that influence soil fertility and help devise management strategies that enhance the sustainability of these areas and thus slow further deforestation. (C) 2007 Elsevier B.V. All rights reserved.

The Soil: Nature, Sustainable Use, Management, and Protection - An Overview

Soil forms the outer skin of the earth's land surface. Often less than a metre in depth, it is essential to sustain natural terrestrial ecosystems and human life. Soils result from the interactions over time between climate, parent material, topography, vegetation, and biota. They vary from place to place. Mineral soils are composed of mineral matter, organic matter, and gas- or liquid-filled pores in varying proportions. Soils perform a wide range of functions and provide many ecosystem or environmental services; with the climate problem, the soil is increasingly being recognised as a potential sink for carbon from the atmosphere. In part because of humankind's (over)use of soils and in part because of natural and human-induced environmental change, there is a widespread decline in soil quality and an increasing number of threats to soil, which jeopardise both the soil's natural functions and its use by humans. As a limited resource, soils must be used sustainably. Soil protection strategies have been indirectly embodied in a number of United Nations conventions, and there are now national and supranational developments towards specific regulations and legislation to protect soils and their functions.

The fate and toxicity of the flavonoids naringenin and formononetin in soil

The flavonoid class of plant secondary metabolites play a multifunctional role in below-ground plant-microbe interactions with their best known function as signals in the nitrogen fixing legume-rhizobia symbiosis. Flavonoids enter rhizosphere soil as a result of root exudation and senescence but little is known about their subsequent fate or impacts on microbial activity. Therefore, the present study examined the sorptive behaviour, biodegradation and impact on dehydrogenase activity (as determined by iodonitrotetrazolium chloride reduction) of the flavonoids naringenin and formononetin in soil. Organic carbon normalised partition coefficients, log K-oc, of 3.12 (formononetin) and 3.19 (naringenin) were estimated from sorption isotherms and, after comparison with literature log K-oc values for compounds whose soil behaviour is better characterised, the test flavonoids were deemed to be moderately sorbed. Naringenin (spiked at 50 mu g g(-1)) was biodegraded without a detectable lag phase with concentrations reduced to 0.13 +/- 0.01 mu g g(-1) at the end of the 96 h time course. Biodegradation of formononetin proceeded after a lag phase of similar to 24 with concentrations reduced to 4.5 +/- 1% of the sterile control after 72 h. Most probable number (MPN) analysis revealed that prior to the addition of flavonoids, the soil contained 5.4 x 10(6) MPNg(-1) (naringenin) and 7.9 x 10(5) MPNg(-1) (formononetin) catabolic microbes. Formononetin concentration had no significant (p > 0.05) effect on soil dehydrogenase activity, whereas naringenin concentration had an overall but non-systematic impact (p = 0.045). These results are discussed with reference to likely total and bioavailable concentrations of flavonoids experienced by microbes in the rhizosphere. (c) 2007 Elsevier Ltd. All rights reserved.

Climate vs. soil factors in local adaptation of two common plant species

Evolutionary theory suggests that divergent natural selection in heterogeneous environments can result in locally adapted plant genotypes. To understand local adaptation it is important to study the ecological factors responsible for divergent selection. At a continental scale, variation in climate can be important while at a local scale soil properties could also play a role. We designed an experiment aimed to disentangle the role of climate and ( abiotic and biotic) soil properties in local adaptation of two common plant species. A grass (Holcus lanatus) and a legume ( Lotus corniculatus), as well as their local soils, were reciprocally transplanted between three sites across an Atlantic-Continental gradient in Europe and grown in common gardens in either their home soil or foreign soils. Growth and reproductive traits were measured over two growing seasons. In both species, we found significant environmental and genetic effects on most of the growth and reproductive traits and a significant interaction between the two environmental effects of soil and climate. The grass species showed significant home site advantage in most of the fitness components, which indicated adaptation to climate. We found no indication that the grass was adapted to local soil conditions. The legume showed a significant home soil advantage for number of fruits only and thus a weak indication of adaptation to soil and no adaptation to climate. Our results show that the importance of climate and soil factors as drivers of local adaptation is species-dependent. This could be related to differences in interactions between plant species and soil biota.

Trophic interactions in a changing world: modelling aboveground-belowground interactions

The rate and scale of human-driven changes can exert profound impacts on ecosystems, the species that make them up and the services they provide that sustain humanity. Given the speed at which these changes are occurring, one of society's major challenges is to coexist within ecosystems and to manage ecosystem services in a sustainable way. The effect of possible scenarios of global change on ecosystem services can be explored using ecosystem models. Such models should adequately represent ecosystem processes above and below the soil surface (aboveground and belowground) and the interactions between them. We explore possibilities to include such interactions into ecosystem models at scales that range from global to local. At the regional to global scale we suggest to expand the plant functional type concept (aggregating plants into groups according to their physiological attributes) to include functional types of aboveground-belowground interactions. At the scale of discrete plant communities, process-based and organism-oriented models could be combined into "hybrid approaches" that include organism-oriented mechanistic representation of a limited number of trophic interactions in an otherwise process - oriented approach. Under global change the density and activity of organisms determining the processes may change non-linearly and therefore explicit knowledge of the organisms and their responses should ideally be included. At the individual plant scale a common organism-based conceptual model of aboveground-belowground interactions has emerged. This conceptual model facilitates the formulation of research questions to guide experiments aiming to identify patterns that are common within, but differ between, ecosystem types and biomes. Such experiments inform modelling approaches at larger scales. Future ecosystem models should better include this evolving knowledge of common patterns of aboveground-belowground interactions. Improved ecosystem models are necessary toots to reduce the uncertainty in the information that assists us in the sustainable management of our environment in a changing world. (C) 2004 Elsevier GmbH. All rights reserved.

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Background: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Results: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. Conclusions: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.

Soil management in relation to sustainable agriculture and ecosystem services

Requirements for research, practices and policies affecting soil management in relation to global food security are reviewed. Managing soil organic carbon (C) is central because soil organic matter influences numerous soil properties relevant to ecosystem functioning and crop growth. Even small changes in total C content can have disproportionately large impacts on key soil physical properties. Practices to encourage maintenance of soil C are important for ensuring sustainability of all soil functions. Soil is a major store of C within the biosphere – increases or decreases in this large stock can either mitigate or worsen climate change. Deforestation, conversion of grasslands to arable cropping and drainage of wetlands all cause emission of C; policies and international action to minimise these changes are urgently required. Sequestration of C in soil can contribute to climate change mitigation but the real impact of different options is often misunderstood. Some changes in management that are beneficial for soil C, increase emissions of nitrous oxide (a powerful greenhouse gas) thus cancelling the benefit. Research on soil physical processes and their interactions with roots can lead to improved and novel practices to improve crop access to water and nutrients. Increased understanding of root function has implications for selection and breeding of crops to maximise capture of water and nutrients. Roots are also a means of delivering natural plant-produced chemicals into soil with potentially beneficial impacts. These include biocontrol of soil-borne pests and diseases and inhibition of the nitrification process in soil (conversion of ammonium to nitrate) with possible benefits for improved nitrogen use efficiency and decreased nitrous oxide emission. The application of molecular methods to studies of soil organisms, and their interactions with roots, is providing new understanding of soil ecology and the basis for novel practical applications. Policy makers and those concerned with development of management approaches need to keep a watching brief on emerging possibilities from this fast-moving area of science. Nutrient management is a key challenge for global food production: there is an urgent need to increase nutrient availability to crops grown by smallholder farmers in developing countries. Many changes in practices including inter-cropping, inclusion of nitrogen-fixing crops, agroforestry and improved recycling have been clearly demonstrated to be beneficial: facilitating policies and practical strategies are needed to make these widely available, taking account of local economic and social conditions. In the longer term fertilizers will be essential for food security: policies and actions are needed to make these available and affordable to small farmers. In developed regions, and those developing rapidly such as China, strategies and policies to manage more precisely the necessarily large flows of nutrients in ways that minimise environmental damage are essential. A specific issue is to minimise emissions of nitrous oxide whilst ensuring sufficient nitrogen is available for adequate food production. Application of known strategies (through either regulation or education), technological developments, and continued research to improve understanding of basic processes will all play a part. Decreasing soil erosion is essential, both to maintain the soil resource and to minimise downstream damage such as sedimentation of rivers with adverse impacts on fisheries. Practical strategies are well known but often have financial implications for farmers. Examples of systems for paying one group of land users for ecosystem services affecting others exist in several parts of the world and serve as a model.

Shoot zinc (Zn) concentration varies widely within Brassica oleracea L. and is affected by soil Zn and phosphorus (P) levels

The low availability of zinc (Zn) in soils and crops affects dietary Zn intake worldwide. This study sought to determine if the natural genetic variation in shoot Zn concentrations (Zn(shoot)) is sufficient to pursue a crop improvement breeding strategy in a leafy vegetable crop. The gene-pool of Brassica oleracea L. was sampled using a large (n = 376) diversity foundation set (DFS), representing almost all species-wide common allelic variation, and 74 commercial varieties (mostly F(1)). The DFS genotypes were grown at low and high soil phosphorus (P) levels under glasshouse and field conditions, and also in a Zn-deficient soil, with or without Zn-fertilisation, in a glasshouse. Despite the large variation in Zn(shoot) among genotypes, environment had a profound effect on Zn(shoot) The heritability of Zn(shoot) was significant, but relatively low, among 90 doubled-haploid (DH) lines from a mapping population. While several quantitative trait loci (QTL) associated with Zn(shoot) occurred on chromosomes C2, C3, C5, C7, and C9, these were generally weak and conditional upon growth conditions. Breeding for Zn(shoot) in B. oleracea is therefore likely to be challenging. Shoot P concentrations increased substantially in all genotypes under low soil Zn conditions. Conversely, only some genotypes had increased Zn(shoot) at low soil P levels. Sufficient natural genetic variation may therefore exist to study some of the interactions between Zn and P nutrition.

The effect of model configuration on modelled hillslope–riparian interactions

The transfer of hillslope water to and through the riparian zone forms a research area of importance in hydrological investigations. Numerical modelling schemes offer a way to visualise and quantify first-order controls on catchment runoff response and mixing. We use a two-dimensional Finite Element model to assess the link between model setup decisions (e.g. zero-flux boundary definitions, soil algorithm choice) and the consequential hydrological process behaviour. A detailed understanding of the consequences of model configuration is required in order to produce reliable estimates of state variables. We demonstrate that model configuration decisions can determine effectively the presence or absence of particular hillslope flow processes and, the magnitude and direction of flux at the hillslope–riparian interface. If these consequences are not fully explored for any given scheme and application, the resulting process inference may well be misleading.

A new data set of soil mineralogy for dust-cycle modeling

The mineralogy of airborne dust affects the impact of dust particles on direct and indirect radiative forcing, on atmospheric chemistry and on biogeochemical cycling. It is determined partly by the mineralogy of the dust-source regions and partly by size-dependent fractionation during erosion and transport. Here we present a data set that characterizes the clay and silt-sized fractions of global soil units in terms of the abundance of 12 minerals that are important for dust–climate interactions: quartz, feldspars, illite, smectite, kaolinite, chlorite, vermiculite, mica, calcite, gypsum, hematite and goethite. The basic mineralogical information is derived from the literature, and is then expanded following explicit rules, in order to characterize as many soil units as possible. We present three alternative realizations of the mineralogical maps, taking the uncertainties in the mineralogical data into account. We examine the implications of the new database for calculations of the single scattering albedo of airborne dust and thus for dust radiative forcing.