Bioinformatic study of the soil microbiome under different cropping systems (original) (raw)
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International Journal of Agronomy
Studies on the physical and chemical effects of extensive grazing on soils have been performed in Colombia, but the effects of dairy cattle rearing on the biological properties of soils are not well known. The objective of this study was to evaluate microorganisms in 48 soils from livestock farms in the highland and lowland tropics in the Northern and Magdalena Medio subregions of the Department of Antioquia (Colombia). Principal component analysis demonstrated differences in the edaphic compositions of the soils, with increased percentages of root colonization by arbuscular mycorrhizal fungi and the density of microorganisms in farms that have soils with moderate phosphorus and nitrogen contents, low potassium content, and a moderately acidic pH. Agglomerative cluster analysis showed two groups for the highland tropic soils and six groups for the lowland tropic soils based on their population densities and interactions with the studied parameters. These results represent a first at...
Atividade microbiológica do solo sob diferentes coberturas vegetais no Cerrado tocantinense
Ciencia Florestal, 2021
The microbial activity is very sensitive to changes in soil cover, making it an important indicator of soil quality. The study aimed to assess changes in soil microbiological activities under different vegetation coverings in the Cerrado biome of Tocantins state. The work was developed in areas of Eucalyptus sp., Pasture, agriculture and Cerrado sensu stricto in the experimental farm of the Federal University of Tocantins. The soil samples were collected in trenches of 70 x 70 cm at depths 0-10 and 10-20 cm, with six replications. The variables evaluated were: concentration and stock in the microbial biomass carbon, basal soil respiration, metabolic quotient and microbial quotient. The statistical analysis was performed using the normality test, analysis of variance and comparison of means by the Tukey test at 5% significance. The area with Eucalyptus sp. at 11 years of age, he had a stable soil microbiological activity, showing stocks in microbial biomass carbon 57.32% higher than ...
PLoS ONE, 2014
Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and notillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than notillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability. Citation: Carbonetto B, Rascovan N, Á lvarez R, Mentaberry A, Vázquez MP (2014) Structure, Composition and Metagenomic Profile of Soil Microbiomes Associated to Agricultural Land Use and Tillage Systems in Argentine Pampas. PLoS ONE 9(6): e99949.
Soil microbial community response to different farm managements in Santa Clara, Cuba
Biotecnología Vegetal, 2016
Siete fincas (dos estatales, dos cooperativas y tres privadas) fueron seleccionadas para evaluar los efectos del manejo agricola en la biomasa microbiana y en la estructura de la comunidad microbiana, asi como, la respuesta a la estacionalidad de estos dos bio-indicadores en los tres sistemas agricolas. Todas las fincas se encontraban sobre suelos pardos con carbonatos. Las muestras fueron colectadas en dos campos de cada finca a una profundidad de 0-20 cm. La comunidad microbiana fue evaluada a traves de dos analisis: carbono de la biomasa microbiana y los fosfolipidos. Las diferencias tecnologicas en el manejo de los suelos, entre los tres sistemas agricolas, afectaron el carbono de la biomasa microbiana y la estructura de la comunidad microbiana. Las diferencias fueron mas pronunciadas entre los sistemas privados y estatales. Los analisis estadisticos demostraron que el total de los fosfolipidos fue significativamente superior en los campos de las cooperativas. El uso del barbech...
Sustainability is the biggest challenge faced by Mexico against a backdrop of bleak environmental degradation. It is necessary to acquire knowledge and to implement environment-friendly alternatives in order to preserve and maintain the natural resources of the country, a key factor in improving the profitability of agricultural production. In nature there is an unknown number of associations between microbial populations, which are influenced by environmental, physical and chemical factors. Microbial relationships determine the dominant or inhibited communities that exist in the soil, in the roots of the plants, and also those that coexist without affecting (positively or negatively) other populations. The factors determining microbial activity are important because of their influence in maintaining soil fertility and crop nutrition. Therefore, this work studied the bacterial populations present in locations with different soil and climatic conditions. This in order to evaluate the...
Soil & Tillage Research, 2007
The objective of this work was to identify soil parameters potentially useful to monitor soil quality under different soil management and crop rotation systems. Microbiological and chemical parameters were evaluated in a field experiment in the State of Paraná, southern Brazil, in response to soil management [no-tillage (NT) and conventional tillage (CT)] and crop rotation [including grain (soybean, S; maize, M; wheat, W) and legume (lupin, L.) and non-legume (oat, O) covers] systems. Three crop rotation systems were evaluated: (1) (OCO 2 -emission rates were similar in NT and CT soils, but plough increased it by an average of 57%. Carbon dioxide emission was 13% higher with lupin residues than with wheat straw; decomposition rates were rapid with both soil management systems. Amounts of microbial biomass carbon and nitrogen (MB-C and MB-N, respectively) were 80 and 104% higher in NT than in CT, respectively; however, in general these parameters were not affected by crop rotation. Efficiency of the microbial community was significantly higher in NT: metabolic quotient (qCO 2 ) was 55% lower than in CT. Soluble C and N levels were 37 and 24% greater in NT than in CT, respectively, with no effects of crop rotation. Furthermore, ratios of soluble C and N contents to MB-C and MB-N were consistently lower in NT, indicating higher immobilization of C and N per unit of MB. The decrease in qCO 2 and the increase in MB-C under NT allowed enhancements in soil C stocks, such that in the 0-40 cm profile, a gain of 2500 kg of C ha À1 was observed in relation to CT. Carbon stocks also varied with crop rotation, with net changes at 0-40 cm of 726, 1167 and À394 kg C ha À1 year, in rotations 1, 2 and 3, respectively. Similar results were obtained for the N stocks, with 410 kg N ha À1 gained in NT, while crop rotations 1, 2 and 3 accumulated 71, 137 and 37 kg of N ha À1 year À1 , respectively. On average, microbial biomass corresponded to 2.4 and 1.7% of the total soil C, and 5.2 and 3.2% of the N in NT and CT systems, respectively. Soil management was the main factor affecting soil C and N levels, but enhancement also resulted from the ratios of legumes and non-legumes in the rotations. The results emphasize the importance of microorganisms as reservoirs of C and N in tropical soils. Furthermore, the parameters associated with microbiological activity were more responsive to soil management and crop rotation effects than were total stocks of C and N, demonstrating their usefulness as indicators of soil quality in the tropics. #
Soil organisms in organic and conventional cropping systems
Scientia Agricola, 2002
Despite the recent interest in organic agriculture, little research has been carried out in this area. Thus, the objective of this study was to compare, in a dystrophic Ultisol, the effects of organic and conventional agricultures on soil organism populations, for the tomato (Lycopersicum esculentum) and corn (Zea mays) crops. In general, it was found that fungus, bacterium and actinomycet populations counted by the number of colonies in the media, were similar for the two cropping systems. CO 2 evolution during the cropping season was higher, up to the double for the organic agriculture system as compared to the conventional. The number of earthworms was about ten times higher in the organic system. There was no difference in the decomposition rate of organic matter of the two systems. In general, the number of microartropods was always higher in the organic plots in relation to the conventional ones, reflectining on the Shannon index diversity. The higher insect population belonged to the Collembola order, and in the case of mites, to the superfamily Oribatuloidea. Individuals of the groups Aranae, Chilopoda, Dyplopoda, Pauropoda, Protura and Symphyla were occasionally collected in similar number in both cropping systems.
OENO One
Rhizosphere microorganisms are considered an extension of plants, representing critical actors involved in the promotion of plant nutrient intake from the surrounding environment. Consequently, a great focus is being made on soil microorganisms since they are considered a promising source for crop resilience improvements under a global climate change scenario. To explore bacterial and fungal communities from arid soils in vineyards and their surroundings from two regions with very different climate and tillage histories, an amplicon sequencing analysis was performed. Specifically, Santa Rosa (SR) is in a region commonly known as the first zone, characterised by low altitude (607 m.a.s.l., Winkler V), while Gualtallary (G) is in the Uco Valley Zone, a region with high altitude (1245 m.a.s.l., Winkler III); both in the productive wine region of Mendoza. SR is characterised by its long cultivation history, while G is a recently cultivated region. Topsoil samples were collected and used...