Phytostabilization of metals in mine soils using Brassica juncea in combination with organic amendments

Background and aims The high metal bioavailability and the poor conditions of mine soils yield a low plant biomass, limiting the application of phytoremediation techniques. A greenhouse experiment was performed to evaluate the effects of organic amendments on metal stabilization and the potential of Brassica juncea L. for phytostabilization in mine soils. Methods Plants were grown in pots filled with soils collected from two mine sites located in Central Spain mixed with 0, 30 and 60 tha?1 of pine bark compost and horse- and sheep-manure compost. Plant biomass and metal concentrations in roots and shoots were measured. Metal bioavailability was assessed using a rhizosphere-based method (rhizo), which consists of a mixture of low-molecular-weight organic acids to simulate root exudates. Results Manure reduced metal concentrations in shoots (10?50 % reduction of Cu and 40?80 % of Zn in comparison with non-amended soils), bioconcentration factor (10?50 % of Cu and 40?80 % of Zn) and metal bioavailability in soil (40?50 % of Cu and 10?30 % of Zn) due to the high pH and the contribution of organic matter. Manure improved soil fertility and was also able to increase plant biomass (5?20 times in shoots and 3?30 times in roots), which resulted in a greater amount of metals removed from soil and accumulated in roots (increase of 2?7 times of Cu and Zn). Plants grown in pine bark treatments and in non-amended soils showed a limited biomass and high metal concentrations in shoots. Conclusions The addition of manure could be effective for the stabilization of metals and for enhancing the phytostabilization ability of B. juncea in mine soils. In this study, this species resulted to be a potential candidate for phytostabilization in combination with manure, differing from previous results, in which B. juncea had been recognized as a phytoextraction plant.

Remediation of crude oil contaminated soils by means of bitumen emulsions

Effective remediation of contaminated sites with oils, heavy metals and other chemical agents is one of the most important environmental problems all over the world. Contaminated soils by petroleum from different sites and origins, might contaminate groundwater aquifers and then be spread by rain. Many years and the requirement of remedial techniques may be needed to remediate them. However, previous experiences show the uselessness of these methods for the solution of all problems. As any case of soil contamination is different, specific studies with relevant factors at financial aspects, legal limits and waste and soil characteristics are needed. In this work, a study of the use of bitumen asphalt emulsion to remediate contaminated soils by crude oils is exposed. By means of the soil stabilization technology, using the contaminated soils as aggregates and the tailor made emulsion as binder, the feasibility of the mix application to produce stable and resistant pavements is demonstrated

Effects of soluble humic acids on the uptake of heavy metals by Vetiveria zizanioides (L.) Nash in contaminated mining soils

In the past, mining wastes were left wherever they might lie in the surroundings of the mine area. Unfortunately, inactive and abandoned mines continue to pollute our environment, reason why these sites should be restored with minimum impact. Phytoextraction is an environmental-friendly and cost-effective technology less harmful than traditional methods that uses metal hyperaccumulator or at least tolerant plants to extract heavy metals from polluted soils. One disadvantage of hyperaccumulator species is their slow growth rate and low biomass production. Vetiveria zizanioides (L.) Nash, perennial species adapted to Mediterranean climate has a strong root system which can reach up to 3 m deep, is fast growing, and can survive in sites with high metal levels (Chen et al., 2004). Due to the fact that metals in abandoned mine tailings become strongly bonded to soil solids, humic acids used as chelating agents could increase metal bioavailability (Evangelou et al., 2004; Wilde et al., 2005) and thereby promote higher accumulation in the harvestable parts of the plant. The objective of this study was to examine the performance of humic acid assisted phytoextraction using Vetiveria zizanioides (L.) Nash in heavy metals contaminated soils.

Carbon dioxide emissions from semi-arid soils amended with biochar alone or combined with mineral and organic fertilizers

Semi-arid soils cover a significant area of Earth s land surface and typically contain large amounts of inorganic C. Determining the effects of biochar additions on CO2 emissions fromsemi-arid soils is therefore essential for evaluating the potential of biochar as a climate change mitigation strategy. Here, we measured the CO2 that evolved from semi-arid calcareous soils amended with biochar at rates of 0 and 20 t ha?1 in a full factorial combination with three different fertilizers (mineral fertilizer, municipal solid waste compost, and sewage sludge) applied at four rates (equivalent to 0, 75, 150, and 225 kg potentially available N ha?1) during 182 days of aerobic incubation. A double exponential model, which describes cumulative CO2 emissions from two active soil C compartments with different turnover rates (one relatively stable and the other more labile), was found to fit verywell all the experimental datasets. In general, the organic fertilizers increased the size and decomposition rate of the stable and labile soil C pools. In contrast, biochar addition had no effects on any of the double exponential model parameters and did not interact with the effects ascribed to the type and rate of fertilizer. After 182 days of incubation, soil organic and microbial biomass C contents tended to increase with increasing the application rates of organic fertilizer, especially of compost, whereas increasing the rate of mineral fertilizer tended to suppress microbial biomass. Biochar was found to increase both organic and inorganic C contents in soil and not to interactwith the effects of type and rate of fertilizer on C fractions. As a whole, our results suggest that the use of biochar as enhancer of semi-arid soils, either alone or combined with mineral and organic fertilizers, is unlikely to increase abiotic and biotic soil CO2 emissions.

Spatial and temporal variations of trace element distribution in soils and street dust of an industrial town in NW Spain: 15 years of study

Extensive spatial and temporal surveys, over 15 years, have been conducted in soil in urban parks and street dusts in one of the most polluted cities in western Europe, Avilés (NW Spain). The first survey was carried out in 1996, and since then monitoring has been undertaken every five years. Whilst the sampling site is a relatively small town, industrial activities (mainly the steel industry and Zn and Al metallurgy) and other less significant urban sources, such as traffic, strongly affect the load of heavy metals in the urban aerosol. Elemental tracers have been used to characterise the influence of these sources on the composition of soil and dust. Although PM10 has decreased over these years as a result of environmental measures undertaken in the city, some of the “industrial” elements still remain in concentrations of concern for example, up to 4.6% and 0.5% of Zn in dust and soil, respectively. Spatial trends in metals such as Zn and Cd clearly reflect sources from the processing industries. The concentrations of these elements across Europe have reduced over time, however the most recent results from Avilés revealed an upward trend in concentration for Zn, Cd, Hg and As. A risk assessment of the soil highlighted As as an element of concern since its cancer risk in adults was more than double the value above which regulatory agencies deem it to be unacceptable. If children were considered to be the receptors, then the risk nearly doubles from this element.

Ranking factors affecting emissions of GHG from incubated agricultural soils

Agriculture significantly contributes to global greenhouse gas (GHG) missions and there is a need to develop effective mitigation strategies. The efficacy of methods to reduce GHG fluxes from agricultural soils can be affected by a range of interacting management and environmental factors. Uniquely, we used the Taguchi experimental design methodology to rank the relative importance of six factors known to affect the emission of GHG from soil: nitrate (NO3?) addition, carbon quality (labile and non-labile C), soil temperature, water-filled pore space (WFPS) and extent of soil compaction. Grassland soil was incubated in jars where selected factors, considered at two or three amounts within the experimental range, were combined in an orthogonal array to determine the importance and interactions between factors with a L16 design, comprising 16 experimental units. Within this L16 design, 216 combinations of the full factorial experimental design were represented. Headspace nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) concentrations were measured and used to calculate fluxes. Results found for the relative influence of factors (WFPS and NO3? addition were the main factors affecting N2O fluxes, whilst glucose, NO3? and soil temperature were the main factors affecting CO2 and CH4 fluxes) were consistent with those already well documented. Interactions between factors were also studied and results showed that factors with Little individual influence became more influential in combination. The proposed methodology offers new possibilities for GHG researchers to study interactions between influential factors and address the optimized sets of conditions to reduce GHG emissions in agro-ecosystems, while reducing the number of experimental units required compared with conventional experimental procedures that adjust one variable at a time.

Fractal parameters of pore space from CT images of soils under contrasting management practices

Soil structure plays an important role in flow and transport phenomena, and a quantitative characterization of the spatial heterogeneity of the pore space geometry is beneficial for prediction of soil physical properties. Morphological features such as pore-size distribution, pore space volume or pore?solid surface can be altered by different soil management practices. Irregularity of these features and their changes can be described using fractal geometry. In this study, we focus primarily on the characterization of soil pore space as a 3D geometrical shape by fractal analysis and on the ability of fractal dimensions to differentiate between two a priori different soil structures. We analyze X-ray computed tomography (CT) images of soils samples from two nearby areas with contrasting management practices. Within these two different soil systems, samples were collected from three depths. Fractal dimensions of the pore-size distributions were different depending on soil use and averaged values also differed at each depth. Fractal dimensions of the volume and surface of the pore space were lower in the tilled soil than in the natural soil but their standard deviations were higher in the former as compared to the latter. Also, it was observed that soil use was a factor that had a statistically significant effect on fractal parameters. Fractal parameters provide useful complementary information about changes in soil structure due to changes in soil management. Read More: http://www.worldscientific.com/doi/abs/10.1142/S0218348X14400118?queryID=%24%7BresultBean.queryID%7D&

Permanent deformation estimates of dynamic equipment foundations: Application to a gas turbine in granular soils

Permanent displacements of a gas turbine founded on a fine, poorly graded, and medium density sand are studied. The amplitudes and modes of vibration are computed using Barkan´s formulation, and the “High-Cycle Accumulation” (HCA) model is employed to account for accumulated deformations due to the high number of cycles. The methodology is simple: it can be easily incorporated into standard mathematical software, and HCA model parameters can be estimated based on granulometry and index properties. Special attention is devoted to ‘transient’ situations at equipment´s start-up, during which a range of frequencies – including frequencies that could be similar to the natural frequencies of the ground – is traversed. Results show that such transient situations could be more restrictive than stationary situations corresponding to normal operation. Therefore, checking the stationary situation only might not be enough, and studying the influence of transient situations on computed permanent displacements is needed to produce a proper foundation design

Risk of Leaching in Soils Amended by Compost and digestate from Municipal Solid Waste

New European directives have proposed the direct application of compost and digestate produced from municipal solid wastes as organic matter sources in agricultural soils. Therefore information about phosphorus leaching from these residues when they are applied to the soil is increasingly mportant. Leaching experiments were conducted to determine the P mobility in compost and digestate mixtures, supplying equivalent amounts to 100 kg P ha?1 to three different types of soils. The tests were performed in accordance with CEN/TS 14405:2004 analyzing the maximum dissolved reactive P and the kinetic rate in the leachate. P biowaste fractionation indicated that digestate has a higher level of available P than compost has. In contrast, P losses in leaching experiments with soil-compost mixtureswere higher than in soil-digestate mixtures. For bothwastes, therewas no correlation between disolved reactive P lost and the water soluble P.The interaction between soil and waste, the long experimentation time, and the volume of leachate obtained caused the waste?s wettability to become an influential parameter in P leaching behavior. The overall conclusion is that kinetic data analysis provides valuable information concerning the sorption mechanism that can be used for predicting the large-scale behavior of soil systems.

Nematodes as indicators of the effect of soil fumigants on soil functioning

Debido al futuro incierto de la mayor parte de los fumigantes edáficos usados actualmente en la Unión Europea, que pueden implicar riesgos para la salud humana/animal y el medio ambiente, es necesario desarrollar programas de manejo integrado para el control de plagas de cultivos. Estos programas se incluyen como obligatorios en el Reglamento (EC) No. 1107/2009. De acuerdo con este Reglamento, es obligatoria la evaluación del riesgo asociado al uso de productos fitosanitarios sobre los organismos edáficos no diana y sus funciones, además de llevar a cabo ensayos con diferentes especies indicadoras para obtener datos de toxicidad que puedan ser usados posteriormente en la evaluación de riesgo. Sin embargo, la baja representatividad de algunas de estas especies indicadoras en el área Mediterránea supone una gran limitación. En esta situación, el Panel Científico de Productos Fitosanitarios y sus Residuos de la Autoridad Europea en Seguridad Alimentaria (EFSA), ha señalado la necesidad de modificar los datos ecotoxicológicos requeridos para evaluar los efectos adversos de los productos fitosanitarios de una manera más integrada, incluyendo criterios funcionales y estructurales mediante organismos como bacterias, hongos, protozoos y nematodos. De este modo, la EFSA ha recomendado el uso de los nematodos en la evaluación de la funcionalidad y estructura del suelo. Los nematodos están globalmente distribuidos y son morfológicamente diversos; esto junto con su gran abundancia y diversidad de respuestas a las perturbaciones edáficas, los convierte en indicadores adecuados del estado del suelo. Puesto que los nematodos interaccionan con muchos otros organismos que participan en diferentes eslabones de la red trófica edáfica, jugando papeles importantes en procesos edáficos esenciales en los agroescosistemas, la diversidad de nematodos es, a menudo, usada como indicador biológico de los efectos de las prácticas agrícolas en el estado del suelo. En los últimos años, diferentes índices basados en la comunidad nematológica han facilitado la interpretación de datos complejos sobre la ecología del suelo. Los índices de la red trófica edáfica, basados en la abundancia de grupos funcionales definidos como grupos C-P y grupos tróficos, permiten la evaluación de la funcionalidad de la red trófica edáfica. Por otra parte, la dificultad en la identificación taxonómica de nematodos para explicar su uso limitado como indicadores ecológicos, es ampliamente discutida, y existe cierta controversia en cuanto a la eficacia de los diferentes métodos de identificación de nematodos. Se argumenta que la identificación morfológica es difícil y puede llevar mucho tiempo debido a la falta de expertos especializados, y se afirma que las técnicas moleculares pueden resolver algunas limitaciones de las técnicas morfológicas como la identificación de juveniles. Sin embargo, los métodos de identificación molecular tienen también limitaciones; la mayoría de las bases de datos de secuencias de ADN están fuertemente orientadas hacia los nematodos fitoparásitos, los cuales representan sólo una parte de la comunidad edáfica de nematodos, mientras que hay poca información disponible de nematodos de vida libre a pesar de representar la mayoría de los nematodos edáficos. Este trabajo se centra en el estudio de los efectos de fumigantes edáficos en la funcionalidad del suelo a través del uso de diferentes indicadores basados en la comunidad de nematodos, como los índices de la red trófica, índices de diversidad, abundancia de los taxones más relevantes etc. También se han analizado otros indicadores funcionales relacionados con la supresividad edáfica, el ciclo de nutrientes o la actividad de la microfauna del suelo. En el capítulo 1, la diversidad de nematodos estudiada en una explotación comercial de fresa y sus alrededores durante dos campañas consecutivas en el suroeste español, fue baja en los suelos fumigados con fumigantes químicos ambas campañas y, aunque se observó una recuperación a lo largo de la campaña en la zona tratada, los suelos fumigados mostraron una condición perturbada permanente. La comunidad de nematodos estuvo más asociada al ciclo de nutrientes en la zona sin cultivar que en los suelos cultivados, y se observó poca relación entre la biomasa de las plantas y la estructura de la comunidad de nematodos. Los surcos sin tratar dentro de la zona de cultivo funcionaron como reservorio tanto de nematodos fitoparásitos como beneficiosos; sin embargo estas diferencias entre los surcos y los lomos de cultivo no fueron suficientes para mantener la supresividad edáfica en los surcos. Los suelos tratados fueron menos supresivos que los suelos sin tratar, y se observaron correlaciones positivas entre la supresividad edáfica y la estructura de la red trófica edáfica y la diversidad de nematodos. En el capítulo 2, se evaluaron los efectos de dos pesticidas orgánicos con efecto nematicida y dos nematicidas convencionales sobre las propiedades físico químicas del suelo, la diversidad de nematodos y la biomasa de las plantas en condiciones experimentales en dos tipos de suelo: suelos agrícolas poco diversos y suelos provenientes de una zona de vegetación natural muy diversos. El mayor efecto se observó en el tratamiento con neem, el cual indujo un gran incremento en el número de dauerlarvas en los suelos pobres en nutrientes, mientras que el mismo tratamiento indujo un incremento de poblaciones de nematodos bacterívoros, más estables y menos oportunistas, en los suelos del pinar ricos en materia orgánica. En el capítulo 3, se comparó la eficacia de métodos moleculares (TRFLP, Terminal Restriction Fragment Length Polymorphism) y morfológicos (microscopía de alta resolución) para la identificación de diferentes comunidades denematodos de España e Irlanda. Se compararon estadísticamente las diferencias y similitudes en la diversidad de nematodos, otros indicadores ecológicos y de la red trófica edáfica. Las identificaciones mediante el uso de TRFLP sólo detectó un porcentaje de los taxones presentes en las muestras de suelo identificadas morfológicamente, y los nematodos omnívoros y predadores no fueron detectados molecularmente en nuestro estudio. Los índices calculados en base a los nematodos micróboros mostraron más similitud cuando se identificaron morfológica y molecularmente que los índices basados en grupos tróficos más altos. Nuestros resultados muestran que, al menos con la técnica usada en este estudio, la identificación morfológica de nematodos es una herramienta fiable y más precisa que la identificación molecular, puesto que en general se obtiene una mayor resolución en la identificación de nematodos. En el capítulo 4, se estudiaron también los efectos de los nematicidas químicos sobre la comunidad de nematodos y la biomasa de las plantas en condiciones experimentales de campo, donde se aplicaron en una rotación de cultivo judía-col durante un ciclo de cultivo. Se aplicaron dos tipos de enmiendas orgánicas con el objetivo de mitigar el efecto negativo de los productos fitosanitarios sobre la diversidad edáfica. El efecto de los nematicidas sobre las propiedades del suelo y sobre la comunidad de nematodos fue más agudo que el efecto de las enmiendas. La incorporación de los restos de cosecha al final del ciclo de cultivo de la judía tuvo un gran efecto sobre la comunidad de nematodos, y aunque el número total de nematodos incrementó al final del experimento, se observó una condición perturbada permanente de la red trófica edáfica a lo largo del experimento. ABSTRACT Due to the uncertain future of the soil fumigants most commonly used in the EU, that might involve risks for human/animal health and the environment, there is a need to develop new integrated pest management programs, included as mandatory in the Regulation (EC) No. 1107/2009, to control crop diseases. According to this Regulation, evaluating the risk associated to the use of the plant production products (PPP) on non-target soil fauna and their function, and developing assays with different indicator species to obtain toxicity data to be used in the risk evaluation is mandatory. However, the low representativeness of some of these indicator species in the Mediterranean area is a relevant limitation. In this situation, the Scientific Panel of Plant Protection Products and their Residues of the European Food Safety Authority (EFSA) has pointed out the necessity of modifying the ecotoxicological data set required to evaluate non-target effects of PPP in a more integrated way, including structural and functional endpoints with organism such as bacteria, fungi, protists and nematodes. Thus, EFSA has recommended the use of nematodes in the assessment of the functional and structural features of the soil. Nematodes are globally distributed and morphologically diverse, and due to their high abundance and diversity of responses to soil disturbance, they are suitable indicators of the soil condition. Since nematodes interact with many other organisms as participants in several links of the soil food web, playing important roles in essential soil processes in agroecosystems, nematode diversity is often used as a biological indicator of the effects of agricultural practices on soil condition. In the last years, various indices based on soil nematode assemblages, have facilitated the interpretation of complex soil ecological data. Soil food web indices based on the abundances of functional guilds defined by C-P groups and trophic groups, permit evaluating soil food web functioning. On the other hand, the difficulty of nematode taxonomical identification is commonly argued to explain their limited used as ecological indicators, and there is a certain controversy in terms of the efficacy of various nematode identification methods. It is argued that the morphological identification is difficult and time consuming due to the lack of specialist knowledge, and it is claimed that molecular techniques can solve some limitations of morphological techniques such as the identification of juveniles. Nevertheless, molecular identification methods are limited too, since most of the DNA-based databases are strongly oriented towards plant-parasitic nematodes that represent only a fraction of the soil nematode community, while there is little information available on free-living nematodes, which represent most soil nematodes. This work focuses on the study of the effects of soil fumigants on soil functioning through the use of different indicators based on soil nematode community as soil food web indices, diversity indices, the abundance of more relevant taxa etc. Other functional indicators related to soil suppressiveness, nutrient cycling, or the activity of soil microfauna have been also studied. In chapter 1, nematode diversity assessed in a commercial strawberry farm and its surroundings for two consecutive growing seasons in southern Spain, was low in fumigated soils with chemical pesticides throughout both seasons and, although yearly recovery occurred within the treated fields, fumigated soils showed a permanent perturbed condition. The nematode community was more closely associated to nutrient cycling in the non-cropped than in the cropped soils, and the link between plant biomass and nematode community structure was weak. Non-treated furrows within the treated fields were a reservoir of both beneficial and plant-parasitic nematodes, but such difference between furrows and beds was not enough to maintain more suppressive soil assemblages in the furrows. Treated soils were less suppressive than unmanaged soils, and there was a positive and significant correlation between soil suppressiveness and soil food web structure and diversity. In chapter 2, the effects of two organic pesticides with nematicide effect and two chemical nematicides on soil physicalchemical properties, soil nematode diversity and plant biomass in experimental conditions were assessed in two types of soils: low diversity soils from an agricultural farm, and high diversity soils from a natural vegetation area. The larger effect was observed on the neem treatment, which induced a large boost of dauer juveniles in the nutrient-depleted soil, while the same treatment induced the increase of more stable, less opportunistic, populations of generalist bacterivore nematodes in the pine forest soil, rich in organic matter. In chapter 3, comparison of the efficiency of molecular (TRFLP, Terminal Restriction Fragment Length Polymorphism) and morphological (microscopy at high magnification) identification methods was carried out in different nematode communities from five sites of different land uses in Spain and Ireland. Differences and similarities on nematode diversity and other ecological and soil food web indices assessed by both methods, were statistically compared. Molecular identification with TRFLP only detected a percentage of the taxa present in the soil samples identified morphologically, and omnivores and predators were not detected molecularly in our study. Indices involving microbial feeding nematodes were more similar between identification methods than indices involving higher trophic links. Our results show that, at least with the technique used in this study, identifying nematodes morphologically is a reliable and more precise identification tool than molecular identification, since a higher taxonomic resolution is in general obtained compared to TRFLP. In chapter 4, the effect of chemical nematicides on nematode community descriptors and plant biomass was also studied in field conditions in an experimental area in which dazomet and dimethyl disulfide was applied in a bean-cabbage rotation system for a single season. Organic amendments were incorporated into the soil with the aim of mitigate the negative effect of the pesticides on soil diversity. The effect of the nematicides was much more noticeable than the effect of the amendments on soil properties and nematode community descriptors. The incorporation of bean crop residues into the soil at the end of bean crop cycle affected soil nematode community descriptors to a great extent, and although total number of nematodes increased at the end of the experiment, a permanent perturbed soil food web condition was observed along the experiment.

Modeling GHG emissions, N and C dynamics in Spanish agricultural soils.

To date, only few initiatives have been carried out in Spain in order to use mathematical models (e.g. DNDC, DayCent, FASSET y SIMSNIC) to estimate nitrogen (N) and carbon (C) dynamics as well as greenhouse gases (GHG) in Spanish agrosystems. Modeling at this level may allow to gain insight on both the complex relationships between biological and physicochemical processes, controlling the processes leading to GHG production and consumption in soils (e.g. nitrification, denitrification, decomposing, etc.), and the interactions between C and N cycles within the different components of the continuum plant-soil-environment. Additionally, these models can simulate the processes behind production, consumition and transport of GHG (e.g. nitrous oxide, N2O, and carbon dioxide, CO2) in the short and medium term and at different scales. Other sources of potential pollution from soils can be identified and quantified using these process-based models (e.g. NO3 y NH3).

Native bradyrhizobial symbionts of Lupinus mariae-josephae, a unique endemism thriving in alkaline soils in Eastern Spain

Lupinus mariae-josephae (Lmj) es una especie de lupino endémica de una pequeña y específica área de Comunidad Valenciana (Este de España), donde prospera en suelos alcalinoscalcáreos, un hábitat singular para los altramuces, que crecen preferentemente en suelos ácidos o neutros. Esto hace de Lmj una especie de lupino única. Cuando se inició este trabajo, la extensión conocida de este endemismo abarcaba unos 700 kilómetros cuadrados, confinados en la provincia de Valencia. En esta área, Lmj prospera en pequeñas poblaciones aisladas que contienen un número reducido de plantas por lo que se la consideró una especie en peligro de extinción. Todos los esfuerzos, utilizando estrategias clásicas dirigidas a ampliar el área de crecimiento de Lmj y garantizar su conservación, han tenido un éxito limitado. El trabajo que se presenta está dirigido a mejorar el conocimiento de la ecología de Lmj, en particular la interacción simbiótica que establece con bacterias del suelo denominadas rizobios y se centra en la caracterización fenotípica, filogenética y genómica de esos rizobios. También se investiga la posible contribución de la simbiosis en mejorar la conservación de Lmj. Para este fin, se han estudiado diferentes aspectos que se describen a continuación. El primero objetivo se centró en aislar y estudiar de la diversidad genética de las bacterias endosimbióticas de Lmj. . Se realizó un análisis filogenético de genes esenciales que mostró que las cepas de Lmj pertenecen al género Bradyrhizobium y que presentan una gran diversidad con características fenotípicas y simbióticas diferentes de cepas de Bradyrhizobium que nodulan otras especies de lupinos nativos de España (cepas ISLU). Las cepas estudiadas se dividieron en dos grupos (Clado I y Clado II). El Clado I, incluye a las cepas Lmj, definiendo un nuevo linaje, filogenéticamente relacionado con otras especies de Bradyrhizobium, como B. jicamae y B. elkanii. El Clado II contiene cepas ISLU relacionadas con cepas de B. canariense y B. japonicum que establecen simbiosis con lupinos de suelos ácidos. Otro análisis filogenético basado en genes simbióticos, distribuyó las cepas de Lmj en sólo dos grupos diferentes. La singularidad y gran diversidad de estas cepas en una pequeña área geográfica, hacen de este, un atractivo sistema para el estudio de la evolución y adaptación de las bacterias simbióticas a su respectiva planta huésped. Adicionalmente, se estudio la presencia de bacterias capaces de nodular Lmj en suelos básicos de Chiapas, México. Sorprendentemente, estos suelos contienen bacterias capaces establecer interacciones simbióticas eficientes con Lmj en ensayos de invernadero. A continuación se investigó la taxonomía de los endosimbiontes de Lmj analizando la secuencia de cuatro genes esenciales (16S rRNA, recA, glnII y atpD) y el promedio de identidad de nucleótidos de genomas completos de algunas cepas representativas de la diversidad (ANIm). Se identificaron nuevas especies de Bradyrhizobium dentro del Clado I y se definió una de ellas: 'Bradyrhizobium valentinum' sp. nov (cepa tipo LmjM3T = CECT 8364T, LMG 2761T). También se abordó cómo conservar Lmj en su hábitat natural mediante inoculación con alguna de las cepas aisladas. Se demostró la ausencia de bacterias capaces de nodular Lmj en suelos rojos alcalinos o ‘‘terra rossa’’ de la Península Ibérica y Baleares. Dos cepas, altamente eficientes en cuanto a la fijación de nitrógeno, LmjC y LmjM3T, fueron seleccionadas para ser empleadas como inoculantes. Dos experimentos de campo llevados a cabo en años consecutivos en áreas con características edafoclimáticas similares a las que presentan las poblaciones de Lmj, lograron la reproducción exitosa de la planta. Se concluyó que un ciclo reproductivo exitoso de Lmj es absolutamente dependiente de la inoculación con sus simbiontes naturales y que la simbiosis debe ser considerada un factor esencial en estrategias de conservación de leguminosas en peligro. La obtención de varias secuencias genómicas de cepas aisladas de Lmj y de otras cepas de Bradyrhizobium reveló una alta similitud entre los genomas de las cepas del Clado I, y permitió la identificación de cinco posibles nuevas especies. Además, se estudiaron tres agrupaciones de genes relacionados con la simbiosis (nod, nif y fix) definiendo un nuevo linaje para las cepas de Lmj, diferente del symbiovar “genistearum” de B. canariense y B. japonicum. La baja diversidad encontrada en el análisis filogenético de los genes simbióticos contrasta con la gran diversidad asociada a genes esenciales. La presencia de plásmidos en cepas del género Bradyrhizobium ha sido descrita en muy pocas ocasiones, sin embargo el análisis de la secuencia genómica de la cepa ISLU101, aislada de Lupinus angustifolius, reveló la presencia de un origen de replicación extracromosómico homólogo al operón repABC, presente en el plásmido de Bradyrhizobium sp BTAi1. Gracias a esta secuencia se identificaron genes homólogos en 19 de 72 cepas ISLU. Filogenéticamente, las secuencias de repABC se agruparon en un grupo monofilético con las de pBTAi1 y separadas de los rizobios de crecimiento rápido. Finalmente, se identificaron sistemas de secreción de proteínas de tipo III (T3SS) en nueve genomas de cepas de Lmj. Los T3SS pueden inyectar proteínas efectoras al interior de células vegetales. Su presencia en rizobios se ha relacionado con la gama de hospedador que pueden nodular y puede tener un efecto beneficioso, neutro o perjudicial en la simbiosis. Los T3SS de las cepas de Lmj codifican para una proteína efectora similar a NopE, un efector dependiente de T3SS descrito en B. diazoefficiens USDA 110T. La proteína NopE de la cepa LmjC se ha caracterizado bioquímicamente. ABSTRACT Lupinus mariae-josephae (Lmj) is a lupine species endemic of a unique small area in Valencia region (Eastern Spain) where the lupine plants thrive in alkaline-limed soils, which preferentially grow in acid or neutral soils. This is the type of soils native lupines of Spain. When this work was initiated, the extension of the endemic area of Lmj was of about 700 squared kilometers confined to the Valencia province. In this area, Lmj thrives in small, isolated patches containing a reduced number of plants, and points to an endemism that can easily became endangered or extinct. Consequently, the Valencia Community authorities gave a ‘‘microreserve” status for conservation of the species. All efforts, using classical strategies directed to extend the area of Lmj growth and ensure its conservation have been so far unsuccessful. The work presented here is directed to improve our knowledge of Lmj ecology and it is centered in the characterization of the rhizobial symbiosis by phenotypic, phylogenetic and genomic analysis as well as in investigate the potential contribution of the symbiosis to improve its conservation. To this end, five different topics have been studied, and results are briefly described here. Extensive details can be followed en the attached, published articles. The first topic deals with the indigenous rhizobial symbionts of the Lmj endemism, and its genetic diversity was investigated. The Lmj root symbionts belong to the Bradyrhizobium genus, and phylogenetic analysis based on core genes identified a large diversity of Bradyrhizobium strains with phenotypic and symbiotic characteristics different from rhizobia nodulating other Lupinus spp. native of Spain. The strains were split in two clades. Clade II contained strains close to classical B. canariense and B. japonicum lineages that establish symbioses with lupines in acid soils of the Mediterranean area. Clade I included Lmj strains that define a new lineage, close to other Bradyrhizobium species as B. jicamae and B. elkanii. The phylogenetic analysis based on symbiotic genes identified only two distinct clusters. The singularity and large diversity of these strains in such a small geographical area makes this an attractive system for studying the evolution and adaptation of the rhizobial symbiont to the plant host. Additionally, the presence of bacteria able to nodulate Lmj in basic soils from Chiapas, Mexico was investigated. Surprisingly, these soils contain bacteria able to effectively nodulate and fix nitrogen with Lmj plants in greenhouse assays. In the second topic, the taxonomic status of the endosymbiotic bacteria of Lmj from Valencia endemism and Chiapas was investigated. Results from phylogenetic analysis of core genes and Average Nucleotide Identity (ANIm) using draft genomic sequences identified new Bradyrhizobium species within strains of Clade I of Lmj endosymbiotic bacteria. Only one of these potentially new species has been defined, meanwhile the others are under process of characterization. The name ‘Bradyrhizobium valentinum’ sp. nov. was proposed for the defined species (type strain LmjM3T= CECT 8364T, LMG 2761T). The third topic was directed to conservation of endangered Lmj in its natural habitat. The relevant conclusion of this experimentation is that the symbiosis should be considered as a relevant factor in the conservation strategies for endangered legumes. First, we showed absence of bacteria able to nodulate Lmj in all the inspected ‘‘terra rossa’’ or alkaline red soils of the Iberian Peninsula and Balearic Islands. Then, two efficient nitrogen fixing strains with Lmj plants, LmjC and LmjM3T, were selected as inoculum for seed coating. Two planting experiments were carried out in consecutive years under natural conditions in areas with edapho-climatic characteristics identical to those sustaining natural Lmj populations, and successful reproduction of the plant was achieved. The relevant conclusion from these assays was that the successful reproductive cycle was absolutely dependent on seedling inoculation with effective bradyrhizobia The forth topic deep into the analysis of the genomic of Lmj representative strains. To this end, draft genomic sequences of selected Lmj strains and type strains of Bradyrhizobium spp. were assembled. The comparison analysis of the draft genomic sequences of Lmj strains and related Bradyrhizobium species grouped in Clade I, revealed a high genomic homology among them, and allowed the definition of five potentially new species of Lmj nodulating bacteria. Also, based on the available draft genomic sequences, only three clusters of nod, fix and nif genes from Lmj strains were identified and showed to define a new symbiotic lineage, distant from that of B. canariense and B. japonicum bv. genistearum. The low diversity exhibited by the phylogenetic analysis of symbiotic genes contrast with the large diversity of strains as regards the housekeeping genes analyzed. Besides, the genomic analysis of a Lupinus angustifolius strain ISLU101, revealed the presence of an extrachromosomal replication origin homologous to repABC cluster from plasmid present in Bradyrhizobium spp BTAi1. This repABC cluster gene sequence allowed the identification of extrachromosomic replication origin in 19 out of 72 Bradyrhizobium strains from Lupinus spp., a highly significant result since the absence of plasmids in the Bradyrhizobium genus was traditionally assumed. The repABC gene sequences of these strains grouped them in a unique monophyletic group, related to B. sp. BTAi1 plasmid, but differentiated from the repABC gene cluster of plasmids in fast growing rhizobium strains. The last topic was focused on characterization of type III secreted effectors present in Lmj endosymbiotic bacteria. Type III secretion systems (T3SS) are specialized protein export machineries which can deliver effector proteins into plant cells. The presence of T3SS in rhizobia has frequently been related to the symbiotic nodulation host-range and may have a beneficial or detrimental effect on the symbiosis with legumes. In this context, the presence of T3SS in genomes of nine Lmj strains was investigated, and it was shown the presence of clusters encoding NopE type III-secreted protein similar to the NopE1 and NopE2 of B. diazoefficiens USDA 110T. The putative NopE protein of LmjC strain is at present being characterized regarding its structure and function.

Ca-amendement and tillage: medium term synergies for improving key soil properties of acid soils. Soil and tillage research, 134: 195-206

Ca-amendments are routinely applied to improve acid soils, whilst no-tillage (NT) has been widely recommended in soils where traditional tillage (TT) has led to losses of organic matter. However, the potential interactions between the two treatments are only partially known. Our study was conducted on an annual forage crop agrosystem with a degraded Palexerult soil located in SW Spain, in order to assess if the combination of NT plus a Ca-amendment provides additional benefits to those of their separate use. To this end we analysed the effects of four different combinations of tillage and Ca-amendment on selected key soil properties, focusing on their relationships. The experimental design was a split-plot with four replicates. The main factor was tillage (NT versus TT) and the second factor was the application or not of a Ca-amendment, consisting of a mixture of sugar foam (SF) and red gypsum (RG). Soil samples were collected from 3 soil layers down to 50 cm after four years of treatment (2009). The use of the Ca-amendment improved pH and Al-toxicity down to 25 cm and increased exchangeable Ca2+ down to 50 cm, even under NT due to the combined effect of SF and RG. Both NT and the Ca-amendment had a beneficial effect on total organic carbon (TOC), especially on particulate organic carbon (POC), in the 0–5 cm layer, with the highest contents observed when both practices were combined. Unlike NT, the Ca-amendment failed to improve soil aggregation in spite of the carbon supplied. This carbon was not protected within the stable aggregates in the medium term, making it more susceptible to mineralization. We suggest that the fraction of Al extracted by oxalate from solid phase (AlOxa-Cu-K) and the glomalin-related soil proteins (GRSPs) are involved in the accumulation of carbon within water stable aggregates, probably through the formation of non-toxic stable Al-OM compounds, including those formed with GRSPs. NT alone decreased AlK in the 0–5 cm soil layer, possibly by increasing POC, TOC and GRSPs, which were observed to play a role in reducing Al toxicity. From our findings, the combination of NT and Ca-amendment appears to be the best management practice to improve chemical and physical characteristics of acid soils degraded by tillage.

Arsenic, antimony and selenium in urban soils: potential risks for human health in urban gardening

The benefits of urban agriculture are many and well documented, ranging from health improvement to community betterment, more sustainable urban development and environment protection. On the negative side, urban soils are commonly enriched in toxic trace elements that have accumulated over time through the deposition of atmospheric particles (generated by automotive traffic, heating systems, historical industrial activities and resuspended street dust), and the uncontrolled disposal of domestic, commercial and industrial wastes. This in turn has given rise to concerns about the level of exposure of urban farmers to these elements and the potential health hazards associated with this exposure. Research efforts in this field have started relatively recently and have almost systematically omitted the influence of Sb and Se, and to a lesser extent of As, although all three have proven toxic effects.