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El presente estudio se realizó en el municipio de Pasto (Nariño, Colombia), con el fin de estimar la cantidad de bacterias oxidadoras de amonio (BOA) y bacterias oxidadoras de nitrito (BON), en tres usos del suelo (bosque secundario, pastura tradicional y sistema silvopastoril) a dos profundidades (0-10 y 10-20 cm). Para ello, se utilizó un diseño experimental completamente al azar (DCA), con seis tratamientos y tres repeticiones, para un total de 18 unidades experimentales; para su estimación, se utilizó la técnica del número más probable (NMP). El análisis de varianza mostró diferencias estadísticas altamente significativas para usos y profundidades del suelo en BOA. La pastura tradicional presentó la mayor densidad de BOA a una profundidad de 0-10 cm: 8,8 × 104 UFC/g, y el bosque presentó menor densidad: 1,3 × 103 UFC/g. En BON, la mayor densidad poblacional se encontró en pastura: 9,4 × 103 UFC/g, y el bosque presentó menor densidad: 3,8 × 103 UFC/g. La mayor densidad de bacterias se presentó de 0 a 10 cm en BOA: 3,7 × 103 UFC/g, mientras que para BON fue de 7,3 × 103 UFC/g, debido posiblemente a que en los primeros 5 cm del suelo se encuentra la capa biológicamente más activa. Las mayores densidades de bacterias nitrificantes encontradas en los usos de suelo: pastura tradicional y sistema silvopastoril, pudieron estar relacionadas con las fertilizaciones orgánicas, reincorporación del estiércol y orina de los animales, que son un sustrato ureico promotor de crecimiento de microorganismos.

La diferenciación rápida de colonias bacterianas es esencial en muchos campos industriales, científicos y de salud humana y animal. Generalmente esa diferenciación se logra por técnicas microscópicas, bioquímicas o genéticas muy elaboradas que requieren tiempo y entrenamiento. En este estudio se utilizaron técnicas de análisis de imágenes sobre patrones de difracción de luz láser para evaluar su sensibilidad en la diferenciación de colonias bacterianas. Adicionalmente se estudió el efecto del tiempo de crecimiento de las colonias en la generación de estos patrones y se determinó la influencia de la cantidad de medio de cultivo en la difracción de luz láser. Los patrones de difracción del láser se obtuvieron sobre cultivos puros de cinco aislamientos bacterianos B1, B2, B3, B2Ca y B2Cb. En la primera prueba de diferenciación se utilizaron colonias de B2, B3, B2Ca. En el estudio del efecto del tiempo de crecimiento sobre patrones de difracción, las bacterias B1 y B2Cb con uno o dos días de crecimiento. Finalmente, el efecto de la cantidad de medio de cultivo en la difracción de la luz, se evaluó en una prueba en cajas petri con 10, 15 o 20 ml de medio de cultivo estéril sin colonias de bacterias. Mediante un análisis de escalado multidimensional realizado con los parámetros de textura extraídos de las imágenes de los patrones, se obtuvo un agrupamiento adecuado de los patrones asociados a las colonias de cada bacteria evaluada, lo cual indicó que las colonias bacterianas se pueden diferenciar por sus patrones de difracción. Adicionalmente se encontró que no hay variaciones significativas en los patrones de difracción obtenidos de dos aislamientos bacterianos en dos tiempos de crecimiento. El espesor del medio de cultivo afectó la difracción del haz de luz pues patrones obtenidos de cajas petri con 10 ml se separan completamente de los patrones obtenidos con 15 y 20 ml, aunque no hay diferencias entre los dos últimos volúmenes. Los resultados indican que esta técnica sencilla parece ser altamente sensible para diferenciar colonias bacterianas en medios de cultivo, y su refinamiento e implementación para investigación o uso industrial podría lograrse a partir de materiales fácilmente disponibles a nivel local.

The roots of most plants are colonized by symbiotic fungi to form mycorrhiza, which play a critical role in the capture of nutrients from the soil and therefore in plant nutrition.Mycorrhizal Symbiosis is recognized as the definitive work in this area.

Organic acids, such as malate, citrate and oxalate, have been proposed to be involved in many processes operating in the rhizosphere, including nutrient acquisition and metal detoxification, alleviation of anaerobic stress in roots, mineral weathering and pathogen attraction. A full assessment of their role in these processes, however, cannot be determined unless the exact mechanisms of plant organic acid release and the fate of these compounds in the soil are more fully understood. This review therefore includes information on organic acid levels in plants (concentrations, compartmentalisation, spatial aspects, synthesis), plant efflux (passive versus active transport, theoretical versus experimental considerations), soil reactions (soil solution concentrations, sorption) and microbial considerations (mineralization). In summary, the release of organic acids from roots can operate by multiple mechanisms in response to a number of well-defined environmental stresses (e.g., Al, P and Fe stress, anoxia): These responses, however, are highly stress-and plant-species specific. In addition, this review indicates that the sorption of organic acids to the mineral phase and mineralisation by the soil's microbial biomass are critical to determining the effectiveness of organic acids in most rhizosphere processes.

Soil samples were collected at alluvial sites of the Litavka River, which flows through the Beroun and Příbram cities in Central Bohemia Region of the Czech Republic in 2005 and 2006. Higher heavy metal content in soils (Cd, Pb, Zn, Cu) is due to composition of the parent rock, emissions from lead processing industry and the leak of toxic material from the steel works sludge ponds in the 1970s and 1980s. The samples were collected from six sites located at different distances from the contamination source (the former sludge ponds) and chemical and biological properties were determined. The ratio of the microbial biomass carbon to oxidisable carbon content dropped down significantly on more heavily contaminated sites. Basal respiration activity did not correlate with the content of heavy metals in soil, but there was certain declining tendency with increasing intensity of soil contamination. Respiration activities significantly correlated with the total carbon, oxidisable carbon and the total nitrogen content. The metabolic quotient showed higher values with increasing contamination. Dehydrogenases and arylsulphatase activities decreased with increasing contamination. Urease activity has also a declining tendency but its relation to different intensity of contamination was not unambiguous. Urease activity has shown a relationship with the content of total nitrogen in soil. No relationship was found between the total sulphur content and arylsulphatase activity. Dehydrogenases, arylsulfatase and urease activities significantly correlated with the microbial biomass carbon.

We review the current knowledge on biodiversity in soils, its role in ecosystem processes, its importance for human purposes, and its resilience against stress and disturbance. The number of existing species is vastly higher than the number described, even in the macroscopically visible taxa, and biogeographical syntheses are largely lacking. A major effort in taxonomy and the training of a new generation of systematists is imperative. This effort has to be focussed on the groups of soil organisms that, to the best of our knowledge, play key roles in ecosystem functioning. To identify such groups, spheres of influence (SOI) of soil biota-such as the root biota, the shredders of organic matter and the soil bioturbators-are recognized that presumably control ecosystem processes, for example, through interactions with plants. Within those SOI, functional groups of soil organisms are recognized. Research questions of the highest urgency are the assignment of species to functional groups and determining the redundancy of species within functional groups. These priorities follow from the need to address the extent of any loss of functioning in soils, associated with intensive agriculture, forest disturbance, pollution of the environment, and global environmental change. The soil biota considered at present to be most at risk are species-poor functional groups among macrofaunal shredders of organic matter, bioturbators of soil, specialized bacteria like nitrifiers and nitrogen fixers, and fungi forming mycorrhizas. An experimental approach in addressing these research priorities is needed, using long-term and large-scale field experiments and modern methods of geostatistics and geographic information systems.

Environmental sustainability is achieved by main-taining and improving soil quality. This quality is defined as “the ability of soil to function” and is evaluated through measuring a minimum set of data corresponding to different soil properties (physical, chemical and biological). However, assessment of these properties does not meet all the conditions necessary to be ideal indicators such as: clearly discriminating between the systems use and / or management evaluation, sensitivity to stress conditions associated with anthropogenic actions, easy measurement, accessibility to many users and short response time. Because loss in quality is associated with the alteration of many processes performed by soil microorganisms they meet the above conditions and have been proposed as valid indicators for diagnosing the impact of changes in land-use and ecosystem restoration. Thus, through the evaluation of the density, activity and /or structure-composition of microorganisms we can determine whether current management systems maintain, improve or degrade the soil. In this article we review the main concepts related to soil quality and its indicators. We discuss the effect of the implementation of silvopastoral systems on soil quality, with an emphasis on the use of microbial indicators.

La dinámica poblacional de la especie humana ha llevado a que la explotación de los recursos naturales, en búsqueda de suplir las necesidades alimenticias de los miles de millones de personas que habitan el planeta. Esta necesidad ha llevado a la utilización de materiales de alta eficiencia en la agricultura, variedades vegetales resistentes a plagas y enfermedades con ciclos de producción más cortos, agroquímicos que surten las necesidades nutricionales y provean protección frente factores bióticos adversos (plagas y enfermedades). Sin embargo, estas estrategias utilizadas en la agricultura moderna han generado impactos ambientales negativos que aún no comprendemos. La contaminación de aguas freáticas, eutrofización, aumento de gases de invernadero y acumulación de sustancias toxicas en la cadena trófica, son algunos de los graves problemas que se presentan por el uso indiscriminado de agroquímicos. Como alternativa a la utilización de estas sustancias, se ha propuesto el uso de bacterias rizosféricas que tienen reconocida acción sobre el crecimiento y desarrollo vegetal (PGPR, por sus siglas en ingles). Estas bacterias son capaces de estimular el desarrollo de las plantas de manera directa e indirecta y poseen una serie de mecanismos complejos que interactúan entre sí para establecer relaciones benéficas, especialmente con las raíces de las plantas objetivo. El estudio y entendimiento de las PGPR han sido temas de gran importancia en muchas investigaciones a nivel mundial, por esta razón esta revisión tiene por objetivo hacer una revisión parcial para dar a conocer los mecanismos que poseen las rizobacterias promotoras del crecimiento vegetal en el desarrollo de las plantas, así como el papel que desempeñan en el ciclaje de nutrientes. Palabras clave: nitrógeno, sideróforos, colonización de raíz,microbiología de suelo. The population dynamics of the human race has led to the exploitation of natural resources in search of a way to meet the nutritional needs of the billions of people inhabiting the planet. This need has led to the use of high-efficiency materials in agriculture, plant varieties with shorter production cycles that are also resistant to pests and diseases, and chemicals that provide protection against biotic factors (pests and disease), additionally the nutrients required to grow plants. However, the strategies used in modern agriculture have led to negative environmental impacts that we have yet to fully understand. Groundwater contamination, eutrophication, increased greenhouse gases, and the accumulation of toxic substances in the food chain are some of the serious problems that have arisen worldwide due to the indiscriminate use of agrochemicals. As an alternative to the use of these substances, the use of rhizopheric bacteria has been proposed owing to its known action as plant growth- promoting bacteria (PGPB). These bacteria are able to stimulate plant growth directly and indirectly and have several complex mechanisms that interact with each other to establish beneficial relationships, especially with the roots of target plants. The study and understanding of PGPR have been the subjects of great importance in many studies at a global level. This review, therefore, aims to better understand the mechanisms of plant growth-promoting rhizobacteria on plant development and their role in nutrient cycling. Keywords: nitrogen, siderophores, root colonization, microbiology of soil.

A soil community food web model was used to improve the understanding of what factors govern the mineralisation of nutrients and carbon and the decay of dead organic matter. The model derives the rates of C and N mineralisation by organisms by splitting their uptake rate of food resources into a rate at which faeces or prey remains are added to detritus, a rate at which elements are incorporated into biomass, and a rate at which elements are released by organisms as inorganic compounds. The functioning of soil organisms in the mineralisation of C and N was modelled in the soil horizon of a Scots pine forest. The organic horizon was divided into three distinct layers, representing successive stages of decay, i.e. litter, fragmented litter, and humus. Each of the layers had a different, quantitative, biota composition. For each layer the annual C and N mineralisation rates were simulated and compared to observed C and N mineralisation rates from organic matter in stratified litterbags. Simulated C and N mineralisation was relatively close to measured losses of C and N, but the fit was not perfect. Discrepancies between the observed and predicted mineralisation rates are discussed in terms of variation in model parameter values of those organisms that showed the highest contribution to mineralisation rates. The measured, and by the model predicted, significant decrease in mineralisation rates down the profile was not explained by the biomass of the primary decomposers and only partly by the total food web biomass. Modelling results indicated that indirect effects of soil fauna, due to trophic interactions with their resources, are an important explanatory factor. In addition, the analyses suggest that community food web structure is an important factor in the regulation of nutrient mineralisation. The model provided the means to evaluate the contribution of functionally defined groups of organisms, structured in a detrital food web, to losses of C and N from successive decay stages.

Today, 12 years after the first field release of a genetically modified plant (GMP), over 15 000 field trials at different locations have been performed. As new and unique characteristics are frequently introduced into GMPs, risk assessment has to be performed to assess their ecological impact. The possibilities of horizontal gene transfer (HGT; no parent-to-offspring transfer of genes) from plants to microorganisms are frequently evaluated in such risk assessments of GMPs before release into the field. In this review we indicate why putative HGT from plants to terrestrial (soil and plant associated) bacteria has raised concern in biosafety evaluations. Further, we discuss possible pathways of HGT from plants to bacteria, outline the barriers to HGT in bacteria, describe the strategies used to investigate HGT from plants to bacteria and summarize the results obtained. Only a few cases of HGT from eukaryotes such as plants to bacteria have been reported to date. These cases have been ascertained after comparison of DNA sequences between plants and bacteria. Although experimental approaches in both field and laboratory studies have not been able to confirm the occurrence of such HGT to naturally occurring bacteria, recently two studies have shown transfer of marker genes from plants to bacteria based on homologous recombination. The few examples of HGT indicated by DNA sequence comparisons suggest that the frequencies of evolutionarily successful HGT from plants to bacteria may be extremely low. However, this inference is based on a small number of experimental studies and indications found in the literature. Transfer frequencies should not be confounded with the likelihood of environmental implications, since the frequency of HGT is probably only marginally important compared with the selective force acting on the outcome. Attention should therefore be focused on enhancing the understanding of selection processes in natural environments. Only an accurate understanding of these selective events will allow the prediction of possible consequences of novel genes following their introduction into open environments.