Heitor Luiz da Costa Coutinho

Evaluation of the diversity of rhizobia in Brazilian agricultural soils cultivated with soybeans

The diversity of rhizobia in agricultural soils planted with soybean (Glycine max L.) and managed under conventional or notillage practices was evaluated by using a combination of trap-host capture and DNA fingerprinting approaches. Fifty-eight rhizobia isolates were captured using pigeonpea (Cajanus cajan L.) as a trap-host and characterised by using the RAPD DNA fingerprinting technique, yielding 25 different RAPD profiles. The application of the Shannon‐Weaver diversity index demonstrated that the diversity of rhizobia was significantly reduced in soil samples from plots cultivated with soybean compared with original uncultivated pasture plots. # 1999 Elsevier Science B.V. All rights reserved.

Effect of Sugarcane Burning or Green Harvest Methods on the Brazilian Cerrado Soil Bacterial Community Structure

Background The Brazilian Cerrado is one of the most important biodiversity reservoirs in the world. The sugarcane cultivation is expanding in this biome and necessitates the study of how it may impact the soil properties of the Cerrado. There is a lack of information especially about the impacts of different sugarcane management on the native bacterial communities of Cerrado soil. Therefore, our objective was to evaluate and compare the soil bacterial community structure of the Cerrado vegetation with two sugarcane systems. Methods We evaluated samples under native vegetation and the impact of the two most commonly used management strategies for sugarcane cultivation (burnt cane and green cane) on this diversity using pyrosequencing and quantitative PCR of the rrs gene (16S rRNA). Results and Conclusions Nineteen different phyla were identified, with Acidobacteria (≈35%), Proteobacteria (≈24%) and Actinobacteria (≈21%) being the most abundant. Many of the sequences were represented by few operational taxonomic units (OTUs, 3% of dissimilarity), which were found in all treatments. In contrast, there were very strong patterns of local selection, with many OTUs occurring only in one sample. Our results reveal a complex bacterial diversity, with a large fraction of microorganisms not yet described, reinforcing the importance of this biome. As possible sign of threat, the qPCR detected a reduction of the bacterial population in agricultural soils compared with native Cerrado soil communities. We conclude that sugarcane cultivation promoted significant structural changes in the soil bacterial community, with Firmicutes phylum and Acidobacteria classes being the groups most affected.

Discrimination of Rhizobium tropici and R. leguminosarum strains by PCR-specific amplification of 16S–23S rDNA spacer region fragments and denaturing gradient gel electrophoresis (DGGE)

With the aim of detecting Rhizobium species directly in the environment, specific PCR primers for Rh. tropici and Rh. leguminosarum were designed on the basis of sequence analysis of 16S–23S rDNA spacer regions of several Rh. tropici, Rh. leguminosarum and Agrobacterium rhizogenes strains. Primer specificity was checked by comparison with available rDNA spacer sequences in databases, and by PCR using DNA from target and reference strains. Sequence polymorphisms of rDNA spacer fragments among strains of the same species were detected by denaturing gradient gel electrophoresis (DGGE). The specific PCR primers designed in this study could be applied to evaluate the diversity of Rh. tropici and Rh. leguminosarum by analysing the polymorphisms of 16S–23S spacer rDNA amplified from either whole‐cell or soil‐extracted DNA.

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

BackgroundSugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated.ResultsOur results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities.ConclusionSugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree.

Análise discriminante de solos sob diferentes usos em área de Mata Atlântica a partir de atributos da matéria orgânica

In the mountain region of the State of Rio de Janeiro (Atlantic Rain Forest biome), small farmers practice shifting cultivation in the slash and burn system. In this work, soil surfaces samples (0-15cm) of a Yellow Red Latossolo under five different vegetal coverings (Atlantic Rain Forest, annual culture, coffee, banana and pasture), had been taken in the small farming area of Bom Jardim RJ for soil chemical characterization and carbon content analysis in the different humic fractions. The samples taken under forest and pasture could be clearly isolated from the other groups for the discriminante model created. For the banana, coffee and culture groups, a certain overlapping was observed, indicating a similarity of the soil organic matter attributes between these coverings. The model allowed to correctly classify 88% of the analyzed samples. The fulvic acid (AF), organic carbon (C), total nitrogen (N), and the C/N ratio had been selected by the model, with the fulvic acids having the attribute of higher relative weight. This result suggests that the humic acids fractionation allows the detection of alterations in the soil that are not possible to be identified for the simple determination of the total organic carbon. The discriminate pattern of areas (forest-pasture and banana-coffe-culture) denotes that fertilizer could be related with changes in some important indicator attributes such as fulvic acids.

Sugarcane trash levels in soil affects the fungi but not bacteria in a short-term field experiment

The sugarcane in Brazil is passing through a management transition that is leading to the abolition of pre-harvest burning. Without burning, large amounts of sugarcane trash is generated, and there is a discussion regarding the utilization of this biomass in the industry versus keeping it in the field to improve soil quality. To study the effects of the trash removal on soil quality, we established an experimental sugarcane plantation with different levels of trash over the soil (0%, 50% and 100% of the original trash deposition) and analyzed the structure of the bacterial and fungal community as the bioindicators of impacts. The soil DNA was extracted, and the microbial community was screened by denaturing gradient gel electrophoresis in two different seasons. Our results suggest that there are no effects from the different levels of trash on the soil chemistry and soil bacterial community. However, the fungal community was significantly impacted, and after twelve months, the community presented different structures among the treatments.

An evaluation of knowledge-based interpretation applied to low-resolution satellite images

The present paper presents the preliminary results of a research aiming at evaluating the potential of knowledge-based approaches for the interpretation of low-resolution satellite images. This work applies a knowledge-based image interpretation system, so-called GEOAIDA, developed at the University of Hannover, Germany, which hires semantic networks and external operators to model the knowledge basis as well as takes advantage of additional data from geographic information systems, GIS. GEOAIDA is used to perform automatically the post-editing, one of the steps of visual interpretation, aiming at mimicking the reasoning of a trained photo-interpreter when he refines the result of a pixel classification procedure. The results obtained hitherto show that the use of knowledge-based approaches for this purpose is promising and, in the future, can be used to automate the post-editing.

Systematics of Legume Nodule Nitrogen Fixing Bacteria

Biological nitrogen fixation (BNF) is easily the most studied microbial process applied to agriculture. It consists of the reduction of atmospheric dinitrogen (N2), unavailable to higher plants, into ammonium (NH4+), an assimilable form of this nutrient. The BNF process is performed solely by microorganisms, the majority inhabiting the soil ecosystem, and is considered to be the most relevant component of the global nitrogen cycle (Ishizuka, 1992). The best known diazotrophs (dinitrogen fixing bacteria) are rhizobia, which are able to establish a symbiotic relationship with plants of the family Leguminosae, hereby called legumes. This symbiosis is characterized by a highly specific association between plant and bacteria. Particular varieties of legume species recognize specific strains of rhizobia, which are able to infect the legume roots. This process triggers the expression of certain plant genes, resulting in the development of nodules around the site of invasion. In the interior of the nodules the bacteria undergo morphological and physiological transformations, becoming nitrogen fixing bacteroides and supplying the plant with nutrient in exchange for carbon-rich material derived from plant photosynthesis.

Adaptation of Soybean Bradyrhizobia to the Brazilian Edaphic Savannahs

The vast Brazilian tropical edaphic savannah, referred to as Cerrado, is considered to be one of the last frontiers of agricultural utilization (xcBorloug and Dowswell, 1994). Soils are deep but leached of nutrients and, in general, strongly acidic (pH averages 5.0 and aluminum is present at toxic levels, xcVerdade, 1971). Agricultural utilization of the Cerrado was stimulated in the sixties when soil amendments, appropriated technologies, and improved/adapted varieties became available. To bring the land to crop production requires a ritual that includes land clearance (dragging or slash and burning of the native vegetation), ploughing, liming, and fertiliser application. In a little over two decades, the Cerrado became a major grain producing area, reducing social pressures threatening the very fragile soils of the Amazon region.