A simple boiling-based DNA extraction for RAPD profiling of landfarm soil to provide representative metagenomic content

Landfarm soils are employed in industrial and petrochemical residue bioremediation. This process induces selective pressure directed towards microorganisms capable of degrading toxic compounds. Detailed description of taxa in these environments is difficult due to a lack of knowledge of culture conditions required for unknown microorganisms. A metagenomic approach permits identification of organisms without the need for culture. However, a DNA extraction step is first required, which can bias taxonomic representativeness and interfere with cloning steps by extracting interference substances. We developed a simplified DNA extraction procedure coupled with metagenomic DNA amplification in an effort to overcome these limitations. The amplified sequences were used to generate a metagenomic data set and the taxonomic and functional representativeness were evaluated in comparison with a data set built with DNA extracted by conventional methods. The simplified and optimized method of RAPD to access metagenomic information provides better representativeness of the taxonomical and metabolic aspects of the environmental samples.

Amycolatopsis thermophila sp nov and Amycolatopsis viridis sp nov., thermophilic actinomycetes isolated from arid soil

The taxonomic positions of two thermophilic actinomycetes isolated from an arid Australian soil sample were established based on an investigation using a polyphasic taxonomic approach. The organisms had chemical and morphological properties typical of members of the genus Amycolatopsis and formed distinct phyletic lines in the Amycolatopsis methanolica 16S rRNA subclade. The two organisms were distinguished from one another and from the type strains of related species of the genus Amycolatopsis using a range of phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the two isolates be classified in the genus Amycolatopsis as Amycolatopsis thermophila sp. nov. (type strain GY088(T)=NCIMB 14699(T)=NRRL B-24836(T)) and Amycolatopsis viridis sp. nov. (type strain GY115(T)=NCIMB 14700(T)= NRRL B-24837(T)).

Iron solubility in mineral dust and aerosol generated from soil samples

Máster Universitario en Oceanografía

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

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

Isolation of plant growth promoting bacteria from torch lake sediments and their role in phytoremediation of metal contaminated soil

In this study, we isolated eight copper-resistant bacteria from Torch Lake sediment contaminated by copper mine tailings (stamp sand). Sequence analysis of gyrB and rpoD genes revealed that these organisms are closer to various Pseudomonas species. These eight bacterial isolates were also resistant to zinc, cesium, lead, arsenate and mercury. Further characterization showed that all the strains produced plant growth promoting indole-3-acetic acid (IAA), iron chelating siderophore and solubilized mineral phosphate and metals. The effect of bacterial inoculation on plant growth and copper uptake by maize (Zea mays) and sunflower (Helianthus annuus) was investigated using one of the isolates (Pseudomonas sp. TLC 6-6.5-4) with higher IAA production and phosphate and metal soubilization, which resulted in a significant increase in copper accumulation in maize and sunflower, and an increase in the total biomass of maize. Genes involved in copper resistance of Pseudomonas sp. TLC 6-6.5-4 was analyzed by transposon mutational analysis. Two copper sensitive mutants with significant reduction in copper resistance were identified: CSM1, a mutant disrupted in trp A gene (tryptophan synthase alpha subunit); CSM2, a mutant disrupted in clpA gene (ATP-dependent Clp protease). Proteomic and metabolomic analysis were performed to identify biochemical and molecular mechanisms involved in copper resistance using CSM2 due to its lower minimum inhibitory concentration compared with CSM1 and the wild type. The effect of different bacterial inoculation methods on plant growth, copper uptake and soil enzyme activities was investigated. Four different delivery methods were used including soil inoculation (before or after plant emergence), seed coating and root dipping. Soil inoculation before sowing seeds and coating seeds with PGPB led to better growth of maize, higher copper uptake and an increase in soil invertase and dehydrogenase activities. Proteomic and metabolomic analyses were performed to investigate the effect of bacterial inoculation on maize grown in normal soil and stamp sand. Our results revealed that bacterial inoculation led to environment-dependent effects on maize proteome and metabolome.

Help from under ground: soil biota facilitate knotweed invasion

Soil biota can be important drivers of plant community structure. Depending on the balance between antagonistic and mutualistic interactions, they can limit or promote the success of plant species. This is particularly important in the context of exotic plant invasions where soil biota can either increase the biotic resistance of habitats, or they can shift the balance between exotic and native plants towards the exotics and thereby greatly contribute to their dominance. Here, we explored the role of soil biota in the invasion success of exotic knotweed (Fallopia × bohemica), one of the world's most noxious invasive plants. We created artificial native plant communities that were experimentally invaded by knotweed, using a range of substrates where we manipulated different fractions of soil biota. We found that invasive knotweed benefited more from the overall presence of soil biota than any of the six native species. In particular the presence of the full natural soil biota strongly shifted the competitive balance in favor of knotweed. Soil biota promoted both regeneration and growth of the invader, which suggests that soil organisms may be important both in the early establishment of knotweed and possibly its later dominance of native communities. Addition of activated carbon to the soil made the advantage of knotweed disappear, which suggests that the mechanisms underlying the positive soil biota effects are chemically mediated. Our study demonstrates that soil organisms play a key role in the invasion success of exotic knotweed.

Anion exchange membrane soil nitrate predicts turfgrass color and yield.

Desirable nitrogen (N) management practices for turfgrass supply sufficient N for high quality turf while limiting excess soil N. Previous studies suggested the potential of anion exchange membranes (AEMs) for predicting turfgrass color, quality, or yield. However, these studies suggested a wide range of critical soil nitrate-nitrogen (NO3-N) values across sample dates. A field experiment, in randomized complete block design with treatments consisting of nine N application rates, was conducted on a mixed species cool-season turfgrass lawn across two growing seasons. Every 2 wk from May to October, turfgrass color was assessed with three different reflectance meters, and soil NO3-N was measured with in situ AEMs. Cate-Nelson models were developed comparing relative reflectance value and yield to AEM desorbed soil NO3-N pooled across all sample dates. These models predicted critical AEM soil NO3-N values from 0. 45 to 1.4 micro g cm-2 d-1. Turf had a low probability of further positive response to AEM soil NO3-N greater than these critical values. These results suggest that soil NO3-N critical values from AEMs may be applicable across sample dates and years and may serve to guide N fertilization to limit excess soil NO3-N.

Nitrate leaching from Kentucky bluegrass soil columns predicted with anion exchange membranes

Ideal nitrogen (N) management for turfgrass supplies sufficient N for high-quality turf without increasing N leaching losses. A greenhouse study was conducted during two 27-week periods to determine if in situ anion exchange membranes (AEMs) could predict nitrate (NO3-N) leaching from a Kentucky bluegrass (Poa pratensis) turf grown on intact soil columns. Treatments consisted of 16 rates of N fertilizer application, from 0 to 98 kg N ha-1 mo-1. Percolate water was collected weekly and analysed for NO3-N. Mean flow-weighted NO3-N concentration and cumulative mass in percolate were exponentially related (pseudo-R2=0.995 and 0.994, respectively) to AEM desorbed soil NO3-N, with a percolate concentration below 10 mg NO3-N L-1 corresponding to an AEM soil NO3-N value of 2.9 micro g cm-2 d-1. Apparent N recovery by turf ranged from 28 to 40% of applied N, with a maximum corresponding to 4.7 micro g cm-2 d-1 AEM soil NO3-N. Turf colour, growth, and chlorophyll index increased with increasing AEM soil NO3-N, but these increases occurred at the expense of increases in NO3-N leaching losses. These results suggest that AEMs might serve as a tool for predicting NO3-N leaching losses from turf.

Soil characteristics and Collembola and Acari abundance in control and warming plots at Abisco Research Station

Extreme weather events can have negative impacts on species survival and community structure when surpassing lethal thresholds. Extreme winter warming events in the Arctic rapidly melt snow and expose ecosystems to unseasonably warm air (2-10 °C for 2-14 days), but returning to cold winter climate exposes the ecosystem to lower temperatures by the loss of insulating snow. Soil animals, which play an integral part in soil processes, may be very susceptible to such events depending on the intensity of soil warming and low temperatures following these events. We simulated week-long extreme winter warming events - using infrared heating lamps, alone or with soil warming cables - for two consecutive years in a sub-Arctic dwarf shrub heathland. Minimum temperatures were lower and freeze-thaw cycles were 2-11 times more frequent in treatment plots compared with control plots. Following the second event, Acari populations decreased by 39%; primarily driven by declines of Prostigmata (69%) and the Mesostigmatic nymphs (74%). A community-weighted vertical stratification shift occurred from smaller soil dwelling (eu-edaphic) Collembola species dominance to larger litter dwelling (hemi-edaphic) species dominance in the canopy-with-soil warming plots compared with controls. The most susceptible groups to these winter warming events were the smallest individuals (Prostigmata and eu-edaphic Collembola). This was not apparent from abundance data at the Collembola taxon level, indicating that life forms and species traits play a major role in community assembly following extreme events. The observed shift in soil community can cascade down to the micro-flora affecting plant productivity and mineralization rates. Short-term extreme weather events have the potential to shift community composition through trait composition with potentially large consequences for ecosystem development.

Micro-granulometry of sedimentary dykes, Kathmandu basin, Nepal

Soft-sediment deformation structures have been analyzed at six sites of the Kathmandu valley. Microgranulometric study (this Supplement and Fig. 3B of Mugnier et al., Tectonophysics, 2011) reveals that silty levels (60 to 80% silt) favor the development of soft-sediment deformation structures, while sandy levels (60 to 80% sand) are passively deformed. Nonetheless well sorted sand levels (more than 80% sand) generate over-fluid pressure during compaction if located beneath a silty cap, leading to fluidization and dike development. 3-D geometry of seismites indicates a very strong horizontal shearing during their development. Using a physical approach based on soil liquefaction during horizontal acceleration, we show that the fluidization zone progressively grows down-section during the shaking, but does not exactly begin at the surface. The comparison of bed-thickness and strength/depth evolution indicates three cases: i) no soft-sediment deformation occurs for thin (few centimeters) silty beds; ii) the thickness of soft-sediment deformation above sandy beds is controlled by the lithological contrast; iii) the thickness of soft-sediment deformation depends on the shaking intensity for very thick silty beds. These 3 cases are evidenced in the Kathmandu basin. We use the 30 cm-thick soft-sediment deformation level formed during the 1833 earthquake as a reference: the 1833 earthquake rupture zone extended very close to Kathmandu, inducing there MMI IX-X damages. A 90 cm-thick sediment deformation has therefore to be induced by an event greater than MMI X. From a compilation of paleo and historic seismology studies, it is found that the great (M ~ 8.1) historical earthquakes are not characteristic of the greatest earthquakes of Himalaya; hence earthquakes greater than M ~ 8.6 occurred. Kathmandu is located above one of the asperities that laterally limits the extent of mega-earthquake ruptures and two successive catastrophic events already affected Kathmandu, in 1255 located to the west of this asperity and in ~ 1100 to the east.

Stable isotope ratios in shells of marine organisms

Oxygen and carbon isotope analyses have been carried out on calcareous skeletons of important recent groups of organisms. Annual temperature ranges and distinct developmental stages can be reconstructed from single shells with the aid of the micro-sampling technique made possible by modern mass-spectrometers. This is in contrast to the results of earlier studies which used bulk sampIes. The skeletons analysed are from Bermuda, the Philippines, the Persian Gulf and the continental margin off Peru. In these environments, seasonal salinity ranges and thus annual variations in the isotopic composition of the water are small. In addition, environmental parameters are weIl documented in these areas. The recognition of seasonal isotopic variations is dependant on the type of calcification. Shells built up by carbonate deposition at the margin, such as molluscs, are suitable for isotopic studies. Analysis is more difficult where chambers are added at the margin of the shell but where older chambers are simultaneously covered by a thin veneer of carbonate e. g. in rotaliid foraminifera. Organisms such as calcareous algae or echinoderms that thicken existing calcareous parts as weIl as growing in length and breadth are the most difficult to analyse. All organisms analysed show temperature related oxygen-isotope fractionation. The most recent groups fractionate oxygen isotopes in accordance with established d18O temperature relationships (Tab. 18, Fig. 42). These groups are deep-sea foraminifera, planktonic foraminifera, serpulids, brachiopods, bryozoa, almost all molluscs, sea urchins, and fish (otoliths). A second group of organisms including the calcareous algae Padina, Acetabularia, and Penicillus, as weIl as barnacles, cause enrichment of the heavy isotope 18O. Finally, the calcareous algae Amphiroa, Cymopolia and Halimeda, the larger foraminifera, corals, starfish, and holothurians cause enrichment of the lighter isotope 16O. Organisms causing non-equilibrium fractionation also record seasonal temperature variations within their skeletons which are reflected in stable-oxygen-isotope patterns. With the exception of the green algae Halimeda and Penicillus, all organisms analysed show lower d13C values than calculated equilibrium values (Tab. 18, Fig. 42). Especially enriched with the lighter isotope 12C are animals such as hermatypic corals and larger foraminifera which exist in symbiosis with other organisms, but also ahermatypic corals, starfish, and holothurians. With increasing age of the organisms, seven different d13C trends were observed within the skeletons. 1) No d13C variations are observed in deep-sea foraminifera presumably due to relatively stable environmental conditions. 2) Lower d13C values occur in miliolid larger foraminifera and are possibly related to increased growth with increasing age of the foraminifera. 3) Higher values are found in planktonic foraminifera and rotaliid larger foraminifera and can be explained by a slowing down of growth with increasing age. 4) A sudden change to lower d13C values at a distinct shell size occurs in molluscs and is possibly caused by the first reproductive event. 5) A low-high-Iow cycle in calcareous algae is possibly caused by variations in the stage of calcification or growth. 6) A positive correlation between d18O and d13C values is found in some hermatypic corals, all ahermatypic corals, in the septa of Nautilus and in the otoliths of fish. In hermatypic corals from tropical areas, this correlation is the result of the inverse relationship between temperature and light caused by summer cloud cover; in other groups it is inferred to be due to metabolic processes. 7) A negative correlation between d18O and d13C values found in hermatypic corals from the subtropics is explained by the sympathetic relationship between temperature and light in these latitudes. These trends show that the carbon isotope fractionation is controlled by the biology of the respective carbonate producing organisms. Thus, the carbon isotope distribution can provide information on the symbiont-host relationship, on metabolic processes and calcification and growth stages during ontogenesis of calcareous marine organisms.

Vegetation, soil and site characteristics of samples taken along the Yamal Transet in 2007-2008

The overarching goal of the Yamal portion of the Greening of the Arctic project is to examine how the terrain and anthropogenic factors of reindeer herding and resource development combined with the climate variations on the Yamal Peninsula affect the spatial and temporal patterns of vegetation change and how these changes are in turn affecting traditional herding of the indigenous people of the region. The purpose of the expeditions was to collect groundobservations in support of remote sensing studies at four locations along a transect that traverses all the major bioclimate subzones of the Yamal Peninsula. This data report is a summary of information collected during the 2007 and 2008 expeditions. It includes all the information from the 2008 data report (Walker et al. 2008) plus new information collected at Kharasavey in Aug 2008. The locations included in this report are Nadym (northern taiga subzone), Laborovaya (southern tundra = subzone E of the Circumpolar Arctic Vegetation Map (CAVM), Vaskiny Dachi (southern typical tundra = subzone D), and Kharasavey (northern typical tundra = subzone C). Another expedition is planned for summer 2009 to the northernmost site at Belyy Ostrov (Arctic tundra = subzone B). Data are reported from 10 study sites - 2 at Nadym, 2 at Laborovaya, and 3 at Vaskiny Dachi and 3 at Kharasavey. The sites are representative of the zonal soils and vegetation, but also include variation related to substrate (clayey vs. sandy soils). Most of the information was collected along 5 transects at each sample site, 5 permanent vegetation study plots, and 1-2 soil pits at each site. The expedition also established soil and permafrost monitoring sites at each location. This data report includes: (1) background for the project, (2) general descriptions and photographs of each locality and sample site, (3) maps of the sites, study plots, and transects at each location, (4) summary of sampling methods used, (5) tabular summaries of the vegetation data (species lists, estimates of cover abundance for each species within vegetation plots, measured percent ground cover of species along transects, site factors for each study plot), (6) summaries of the Normalized Difference Vegetation Index (NDVI) and leaf area index (LAI) along each transect, (7) soil descriptions and photos of the soil pits at each study site, (8) summaries of thaw measurements along each transect, and (9) contact information for each of the participants. One of the primary objectives was to provide the Russian partners with full documentation of the methods so that Russian observers in future years could repeat the observations independently.

Micro- and picoplankton in waters of the Saint Paul Island, Pribilof Islands, Bering Sea

On the basis of materials collected in June-August 1994 characteristic data on microplankton were gathered in three biotopes of the eastern shelf of the Bering Sea: open shelf (coastal zone), the harbor, and the salt lagoon of Saint Paul Island (Pribiof Islands). The following parameters of microplanktonic communities were analyzed: abundance, biomass, and production of autotrophic picoplankton (picoalgae and cyanobacteria); abundance, biomass, growth rate constant, and production of bacterioplankton; role of filiform bacteria in bacterioplankton; species composition of heterotrophic flagellates and ciliates, their abundance, and biomass. Growth rates and consumption rates of picoplankton and bacterioplankton by heterotrophic nano- and microplankton were estimated in the experiments using the dilution method. Temporal dynamics of all structural and functional parameters of microplankton were analyzed. The minor role of autotrophic picoplankton and significant role of bacterioplankton as well as heterotrophic nano- and microplankton in planktonic communities of studied biotopes during summer months was shown. During certain periods, bacterial biomass was as high as 50-65% of phytoplankton biomass, and production of bacteria was as high as 20-40% of primary production. In the middle of the season biomass of nano- and microheterotrophic organisms in different biotopes exceeded biomass of mesozooplankton 2-10 times. Average consumption of bacterial production by nano- and microplankton during the period of observations was 85-94%.

Thresholding Soil Surface Images

Soil erosion is a complex phenomenon involving the detachment and transport of soil particles, storage and runoff of rainwater, and infiltration. The relative magnitude and importance of these processes depends on several factors being one of them surface micro-topography, usually quanti[U+FB01]ed trough soil surface roughness (SSR). SSR greatly affects surface sealing and runoff generation, yet little information is available about the effect of roughness on the spatial distribution of runoff and on flow concentration. The methods commonly used to measure SSR involve measuring point elevation using a pin roughness meter or laser, both of which are labor intensive and expensive. Lately a simple and inexpensive technique based on percentage of shadow in soil surface image has been developed to determine SSR in the field in order to obtain measurement for wide spread application. One of the first steps in this technique is image de-noising and thresholding to estimate the percentage of black pixels in the studied area. In this work, a series of soil surface images have been analyzed applying several de-noising wavelet analysis and thresholding algorithms to study the variation in percentage of shadows and the shadows size distribution

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.