Novel inorganic pyrophosphatase from soil metagenomic and family and subfamily prediction

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Análise in silico de uma pirofosfatase e de uma tiosterase de uma biblioteca metagenômica de solo de Eucalipto spp

Pós-graduação em Microbiologia Agropecuária - FCAV

MetaPPase by in silico analyses predicting the novel gene operate as H+ pumps.

The lastyears declined the discovery of compounds to use in industrial and naturaldiversity has been the best supplier for novel genes, enzymes and compounds inhigh demand by the biotechnology industry. We know immense diversity of microorganisms,yet most remains unexplored. For these reason we use the metagenômica approach toinvestigate the potential of uncultured microorganisms. With this purpose weused the metagenomic library of from Eucalyptus spp. arboretum (EAA), wedid screening to found positive clone and them was submitted to the process of shotgun,the data obtained was submitted a bioinformatics analyses. Our results showsthe hypothesis of high unexplored microbial diversity of soil are able to foundnovel genes and metagenomic approach is and allowed to isolate novel genes and insilico analyses are essential part to identify a novel Inorganicpyrophosphatase (PPase) prediction indicated the novel gene operate as H+ pumps. Thissuggests that a special feature, our work in situ will be cloning thegene expression vector for subsequent kinetic characterization and crystallization.

Bacterial diversity in soil in response to different plans, phosphate fertilizers and liming

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Bacterial diversity of terra preta and pristine forest soil from the Western Amazon

The survey presented here describes the bacterial diversity and community structures of a pristine forest soil and an anthropogenic, terra preta from the Western Amazon forest using molecular methods to identify the predominant phylogenetic groups. Bacterial community similarities and species diversity in the two soils were compared using oligonucleotide fingerprint grouping of 16S rRNA gene sequences for 1500 clones (OFRG) and by DNA sequencing. The results showed that both soils had similar bacterial community compositions over a range of phylogenetic distances, among which Acidobacteria were predominant, but that terra preta supported approximately 25% greater species richness. The survey provides the first detailed analysis of the composition and structure of bacterial communities from terra preta anthrosols using noncultured-based molecular methods. (c) 2006 Elsevier Ltd. All rights reserved.

Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Molecular analysis of the bacterial diversity in a specialized consortium for diesel oil degradation

Diesel oil is a compound derived from petroleum, consisting primarily of hydrocarbons. Poor conditions in transportation and storage of this product can contribute significantly to accidental spills causing serious ecological problems in soil and water and affecting the diversity of the microbial environment. The cloning and sequencing of the 16S rRNA gene is one of the molecular techniques that allows estimation and comparison of the microbial diversity in different environmental samples. The aim of this work was to estimate the diversity of microorganisms from the Bacteria domain in a consortium specialized in diesel oil degradation through partial sequencing of the 16S rRNA gene. After the extraction of DNA metagenomics, the material was amplified by PCR reaction using specific oligonucleotide primers for the 16S rRNA gene. The PCR products were cloned into a pGEM-T-Easy vector (Promega), and Escherichia coli was used as the host cell for recombinant DNAs. The partial clone sequencing was obtained using universal oligonucleotide primers from the vector. The genetic library obtained generated 431 clones. All the sequenced clones presented similarity to phylum Proteobacteria, with Gammaproteobacteria the most present group (49.8 % of the clones), followed by Alphaproteobacteira (44.8 %) and Betaproteobacteria (5.4 %). The Pseudomonas genus was the most abundant in the metagenomic library, followed by the Parvibaculum and the Sphingobium genus, respectively. After partial sequencing of the 16S rRNA, the diversity of the bacterial consortium was estimated using DOTUR software. When comparing these sequences to the database from the National Center for Biotechnology Information (NCBI), a strong correlation was found between the data generated by the software used and the data deposited in NCBI.

Bacterial functional redundancy along a soil reclamation gradient

A strategy to measure bacterial functional redundancy was developed and tested with soils collected along a soil reclamation gradient by determining the richness and diversity of bacterial groups capable of in situ growth on selected carbon substrates. Soil cores were collected from four sites along a transect from the Jamari tin mine site in the Jamari National Forest, Rondonia, RO, Brazil: denuded mine spoil, soil from below the canopy of invading pioneer trees, revegetated soil under new growth on the forest edge, and the forest floor of an adjacent preserved forest. Bacterial population responses were analyzed by amending these soil samples with individual carbon substrates in the presence of bromodeoxyuridine (BrdU), BrdU-labeled DNA was then subjected to a 16S-23S rRNA intergenic analysis to depict the actively growing bacteria from each site, the number and diversity of bacterial groups responding to four carbon substrates (L-serine, L-threonine, sodium citrate, and or-lactose hydrate) increased along the reclamation-vegetation gradient such that the preserved forest soil samples contained the highest functional redundancy for each substrate. These data suggest that bacterial functional redundancy increases in relation to the regrowth of plant communities and may therefore represent an important aspect of the restoration of soil biological functionality to reclaimed mine spoils. They also suggest that bacterial functional redundancy may be a useful indicator of soil quality and ecosystem functioning.

Soil profile, relief features and their relation to structure and distribution of Brazilian Atlantic rain forest trees

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

An analysis of the floristic composition and diversity of Amazonian forests including those of the Guiana Shield

A large number of newly published and unpublished hectare plots in Amazonia and the Guiana Shield area allow an analysis of family composition and testing of hypotheses concerning alpha-diversity in the south American rain forest. Using data from 94 plots the family-level floristic patterns in wet tropical South America are described. To test diversity patterns, 268 plots are used in this large area. Contrary to a widely held belief, western Amazonian plots are not necessarily the most diverse. Several central Amazonian plots have equal or even higher tree diversity. Annual rainfall is not a good estimator for tree diversity in the Amazonia area and Guiana shield. Plots in the Guiana Shield area (and eastern Amazonia) usually have lower diversity than those in central or western Amazonia. It is argued that this is not because of low rainfall or low nutrient status of the soil but because of the small area of the relatively isolated rain forest area in eastern Amazonia and the Guiana Shield. The low diversity on nutrient-poor white sand soils in the Amazon basin is not necessarily due to their Low nutrient status but is, at least partly, caused by their small extent and fragmented nature.

Soil seed banks in tropical forest fragments with different disturbance histories in southeastern Brazil

Soil seed banks are considered an important mechanism for natural regeneration in tropical forest ecosystems. This paper investigated the soil seed bank in two semideciduous seasonal tropical forest fragments with different disturbance histories in Botucatu, southeastern Brazil. In each study site, 40 superficial soil samples (30 cm × 30 cm × 5 cm) were taken at the end of both the dry and rainy seasons. The seeds were estimated by the germination method. Average soil seed density was 588.6 and 800.3 seeds m-2, respectively, for site 1 (less disturbed) and site 2 (more disturbed). Seed density and diversity (H′) were significantly higher in site 2 in both seasons. Non-woody taxa predominated in both fragments, but pioneer tree species were better represented in the less disturbed forest. Both ecosystems have a potential for regeneration from soil seed banks, but this potential is higher in the less disturbed site. Low richness and density of pioneer tree species in the seed bank indicate that the ecosystem has lost its resilience. The seed bank is not as important in these ecosystems as in other forests. Results indicate that management strategies to restore these forests should take into account the possibility of recovering soil seed bank processes and dynamics. © 2007 Elsevier B.V. All rights reserved.

Ant diversity in a sugarcane culture without the use of straw burning in southeast, são paulo, Brazil

Problem statement: One of the current requirements of agroecosystem management is the maintenance of biodiversity. Manual sugarcane harvesting with the previous burning of straw has been gradually replaced by mechanical harvesting in Brazil. However, the diversity of Formicidae, which can be a natural pest controller, has not been studied in this new system yet. Approach: This study was carried out to assess the diversity of ants in an exclusively mechanically harvested sugarcane culture based on the hypothesis that species richness and abundance will increase with the deposition of straw in this culture system. Ants were sampled using pitfall traps in six sugarcane cultivars during three consecutive harvest cycles. Results: A total of 8,139 ants, distributed in 39 species, were collected. Richness, abundance and diversity differed between harvest cycles, especially in the first cycle, when the soil did not have any straw and in the two last cycles and the straw layer was about 10-15 cm thick. The communities found in the second and third cycles were similar and the maintenance of straw in the culture contributed to a greater species diversity, particularly of generalist predaceous taxa, which may contribute to the natural control of pests. Conclusion: The diversity of ants increased with straw deposition, including of taxa that may be beneficial to the sugarcane culture. However, new studies of the predatory and competition relations in this agroecosystem are necessary. © 2010 Science Publications.

Soil erodibility assessment in a pasture and forest remnant using the inderbitzen device

Brazil has the largest cattle herd in the world with approximately 200 million head. An important feature of the Brazilian cattle industry is that most of its herd is raised on pasture, which constitutes one of the most economical and practical ways to produce and provide food for cattle. However, this production model is mishandled and can lead to soil degradation. Maintaining soil quality is essential for the conservation of natural ecosystems and the areas of production, thus soil quality improves the conditions for biogeochemical cycles. In this context, the objective of this study was to develop a device for testing the Inderbitzen way of assessing soil erodibility in two situations of usage and occupation. Therefore, one area was used as a sample collection occupied by grazing and the other as a forest fragment; both located in the city of Sorocaba in Sao Paulo State, Brazil. Thus, we concluded that the proposed device - the Inderbitzen - proved capable of assessing soil erodibility of the pasture and remnant forest. Accordingly, there was a tendency for a smaller loss of forest soils in the remnant when compared to the degraded pasture. The greatest resistance of the soil erosion in the forest remnant may be associated with the amount of organic matter released by the forest litter in all its diversity, influencing the quality of the structure of aggregates. © 2013 WIT Press.

Frequency and genetic diversity of the MAT1 locus of Histoplasma capsulatum isolates in Mexico and Brazil

The MAT1-1 and MAT1-2 idiomorphs associated with the MAT1 locus of Histoplasma capsulatum were identified by PCR. A total of 28 fungal isolates, 6 isolates from human clinical samples and 22 isolates from environmental (infected bat and contaminated soil) samples, were studied. Among the 14 isolates from Mexico, 71.4% (95% confidence interval [95% CI], 48.3% to 94.5%) were of the MAT1-2 genotype, whereas 100% of the isolates from Brazil were of the MAT1-1 genotype. Each MAT1 idiomorphic region was sequenced and aligned, using the sequences of the G-217B (+mating type) and G-186AR (-mating type) strains as references. BLASTn analyses of the MAT1-1 and MAT1-2 sequences studied correlated with their respective+ and-mating type genotypes. Trees were generated by the maximum likelihood (ML) method to search for similarity among isolates of each MAT1 idiomorph. All MAT1-1 isolates originated from Brazilian bats formed a well-defined group; three isolates from Mexico, the G-217B strain, and a subgroup encompassing all soil-derived isolates and two clinical isolates from Brazil formed a second group; last, one isolate (EH-696P) from a migratory bat captured in Mexico formed a third group of the MAT1-1 genotype. The MAT1-2 idiomorph formed two groups, one of which included two H. capsulatum isolates from infected bats that were closely related to the G-186AR strain. The other group was formed by two human isolates and six isolates from infected bats. Concatenated ML trees, with internal transcribed spacer 1 (ITS1) -5.8S-ITS2 and MAT1-1 or MAT1-2 sequences, support the relatedness of MAT1-1 or MAT1-2 isolates. H. capsulatum mating types were associated with the geographical origin of the isolates, and all isolates from Brazil correlated with their environmental sources. © 2013, American Society for Microbiology. All Rights Reserved.

Sorption and desorption of phosphate on biochar and biochar-soil mixtures

The term biochar refers to materials with diverse chemical, physical and physicochemical characteristics that have potential as a soil amendment. The purpose of this study was to investigate the P sorption/desorption properties of various slow biochars and one fast pyrolysis biochar and to determine how a fast pyrolysis biochar influences these properties in a degraded tropical soil. The fast pyrolysis biochar was a mixture of three separate biochars: sawdust, elephant grass and sugar cane leaves. Three other biochars were made by slow pyrolysis from three Amazonian tree species (Lacre, Ingá and Embaúba) at three temperatures of formation (400 °C, 500 °C, 600 °C). Inorganic P was added to develop sorption curves and then desorbed to develop desorption curves for all biochar situations. For the slow pyrolysis, the 600 oC biochar had a reduced capacity to sorb P (4-10 times less) relative to those biochars formed at 400 °C and 500 °C. Conversely, biochar from Ingá desorbed the most P. The fast pyrolysis biochar, when mixed with degraded tropical mineral soil, decreased the soil's P sorption capacity by 55% presumably because of the high soluble, inorganic P prevalent in this biochar (909 mg P/kg of biochar). Phosphorus desorption from the fast pyrolysis biochar/soil mixture not only exhibited a common desorption curve but also buffered the soil solution at a value of ca. 0.2 mg/L. This study shows the diversity in P chemistry that can be expected when biochar is a soil amendment and suggests the potential to develop biochars with properties to meet specific objectives. © 2013 British Society of Soil Science.