Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes - a genome comparison

The slow-growing genus Bradyrhizobium is biologically important in soils, with different representatives found to perform a range of biochemical functions including photosynthesis, induction of root nodules and symbiotic nitrogen fixation and denitrification. Consequently, the role of the genus in soil ecology and biogeochemical transformations is of agricultural and environmental significance. Some isolates of Bradyrhizobium have been shown to be non-symbiotic and do not possess the ability to form nodules. Here we present the genome and gene annotations of two such free-living Bradyrhizobium isolates, named G22 and BF49, from soils with differing long-term management regimes (grassland and bare fallow respectively) in addition to carbon metabolism analysis. These Bradyrhizobium isolates are the first to be isolated and sequenced from European soil and are the first free-living Bradyrhizobium isolates, lacking both nodulation and nitrogen fixation genes, to have their genomes sequenced and assembled from cultured samples. The G22 and BF49 genomes are distinctly different with respect to size and number of genes; the grassland isolate also contains a plasmid. There are also a number of functional differences between these isolates and other published genomes, suggesting that this ubiquitous genus is extremely heterogeneous and has roles within the community not including symbiotic nitrogen fixation.

EPR, FT-IR and XRD investigation of soils from Parana, Brazil

Samples of Araucaria area soil from Parana state, Brazil, were separated by particle size fractionation and investigated by electron paramagnetic resonance (EPR) in X-Band of 9.5 GHz at room temperature and 77K, infra-red spectroscopy and X-ray diffractometry. The paramagnetic species in the soil samples were identified by comparison with EPR spectra of some minerals studied recently by our group, several soil types and/or soil components investigated in the literature. The value of g = 2.1 (Delta H = 85 mT) indicated the presence of ferrihydrite. Hematite was identified by g = 2.1 (Delta H = 100 mT) and g = 4.3 for Fe(3+) lines of the concentrated dominium and diluted dominium. Kaolinite was identified by IR and EPR with the resonance at g = 4.3 attributed to Fe(3+) ions in isolated sites of tetrahedral and octahedral symmetry with rhombic distortion. The resonances at g = 3.7 and g = 4.9 were attributed to Fe(3+) in more highly symmetrical environment than rhombic symmetry, but not in axial symmetry. Three signals around g = 2 were attributed to radiation defects, plus additional resonances at g = 2.8 and 9.0. Signals less intense than those at g = 2.1, 3.7, and 6.5, observed for clear grains of soil, were attributed to presence of Fe(3+) in quartz which was identified by IR and XDR. (C) 2011 Elsevier B.V. All rights reserved.

Geochemistry of iron and manganese in soils and sediments of a mangrove system, Island of Pai Matos (Cananeia - SP, Brazil)

Five zones along a transect of 180 m were selected for study on the Island of Pai Matos (Sao Paulo, Brazil). Four of the zones are colonised by vascular plants (Spartina SP, Laguncularia LG, Avicennia AV and Rhizophora RH) and were denominated soils, and the other zone, which lacks vegetation, was denominated sediment (SD). The geochemical conditions differed significantly in soils and sediment and also at different depths. The soils were oxic (Eh > 350 mV) or suboxic (Eh: 350-100 mV) at the surface and anoxic (Eh < 100 mV) at depth, whereas in the sediment anoxic conditions prevailed at all depths, but with a lower concentration of sulphides in the pore water and pyrite in the solid fraction. Under these geochemical conditions Fe is retained in the soils, while the Mn tends to be mobilized and lost. The most abundant form of iron oxyhydroxide was lepidocrocite (mean concentration for all sites and depths, 45 +/- 19 mu mol g(-1)), followed by goethite (30 19 mu mol g(-1))and ferrihydrite (19 +/- 11 mu mol g(-1)),with significant differences among the mean concentrations. There was a significant decrease with depth in all the types of Fe oxyhydroxides measured, particularly the poorly crystalline forms. The pyrite fraction was an important component of the free Fe pool (non-silicate Fe) in all soils as well as in the sediment, especially below 20 cm depth (mean concentration for all sites and depths, 60 +/- 54 mu mol CI). Furthermore, the mean concentration of Fe-pyrite for all sites and depths was higher than that obtained for any of the three Fe oxyhydroxides measured. The Fe-AVS was a minor fraction, indicating that the high concentrations of dissolved Fe in the soils in the upper area of the transect result from the oxidation of Fe sulphides during low tide. Mossbauer spectroscopy also revealed that most of the Fe (III) was associated with silicates, in this case nontronite. The presence of crystals of pyrite associated with phyllosilicates in samples from the upper layer of the soils may indicate that pyritization of this form of Fe(III) is more rapid than usually reported for ocean bed sediments. The sequential extraction of Mn did not reveal any clearly dominant fraction, with the Mn-carbonate fraction being the most prevalent, followed by exchangeable Mn and oxides of Mn, whereas pyrite-Mn and Mn associated with crystalline Fe-oxides were present at significantly lower concentrations. The high concentration of dissolved Mn found in the soils in the lower part of the transect is consistent with the fact that the solubility is determined by the carbonate fraction. Unlike for Fe, in the soils in the higher zone, which are subject to intense drainage during low tide, there was loss of Mn, as reflected by the concentration of total Mn. (C) 2008 Elsevier B.V. All rights reserved.

Rock magnetism in soils of the Pampean plain. Buenos Aires province, Argentina. Linking climate and magnetic behaviour

Results of the study of Argiudolls in two localities (Zarate and Veronica) of the Pampean plain, Argentina, are presented in this contribution. This is a typical area covered by loess. The magnetic studies carried out allowed to determine the presence of detrital magnetite and titanomagnetite, as well as maghemite, pedogenic goethite and superparamagnetic particles (SP). In Veronica soils, a depletion of ferromagnetic minerals is recorded The dominant process in these soils has been the reductive loss of detrital magnetite and titanomagnetite. This is associated with a greater degree of evolution of the soil, which is determined by the concentration and type of detected clays. The higher clay concentration in these soils facilitated reducing conditions and a greater loss of detrital magnetic particles. The loss is reinforced under poor drainage conditions. In the poorly drained soil of Zarate, a concentration of magnetic particles is observed in the Bt horizon, which is associated with an illuviation process. The well drained soil of the same locality shows neoformation of SP particles. These particles would have an ephemeral life until a new wet period in the annual cycle occurs. Although some characteristics of the magnetic signal appear reinforced by the conditions of drainage, this aspect does not seem to be too significant, at least in the Pampean region with low topographic gradients.

The Determination of Total Hydrogen, Carbon, Nitrogen and Sulfur in Silicates, Silicate Rocks, Soils and Sediments

Determinations of the volatile elements carbon, hydrogen, sulfur and nitrogen in many geological RM, performed with the LECO CHN and SC analysers, are presented. The method allowed the determination of S in concentrations from a few % m/m to 0.001% m/m or less, of C from % m/m to 0.01% m/m and of H from % m/m to 0.004% m/m. Accuracy was usually better than the XRF method (for S). All obtained values passed the Sutarno-Steger test, which establishes that vertical bar(mean(analysed) - mean(certified))vertical bar/ S(certified) < 2, for the cases with an appropriate number of determinations (n > 10 for each element). It was possible to perform routine determination of C, H and S with the instrumentation, coupled with the determination of major and minor elements in geological materials. Determination of nitrogen could also be performed on an exploratory basis, with improvements in the method dependent on the future availability of more reference materials with reliable composition of this element.

Distribution of Ra-226, Th-232 and K-40 in soils and sugar cane crops at Corumbatai river basin, São Paulo State, Brazil

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

Peat humic substances enriched with nutrients for agricultural applications: Competition between nutrients and non-essential metals present in tropical soils

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Carbon, nitrogen and phosphorus mineralization in two soils amended with distillery yeast

The possibility of using yeast from alcohol distilleries as a source of nutrients in soil was investigated. The following treatments were used: no fertilization (control), 0.5% (w/w) yeast, 1% (w/w) yeast, and NPK. The decomposition of yeast was monitored for 90 days in two soils. The CO, production and the microbial biomass were increased by art average of 1- to 3-fold by yeast incorporation compared to control. Protease activity also was enhanced 3- to 8-fold in the soils supplemented with yeast compared to control. The phosphatase activities were higher than control only during the first days. While nitrate contents increased in all treatments compared to control, available P only increased in the soils amended with 1%, yeast or NPK by 45-119% and 309-489%, respectively. These results indicate that there exists an excellent potential for the use of yeast in the soil as a source of nitrate and available P for plant nutrition. (C) 2003 Elsevier Ltd. All rights reserved.

Soil sampling intensity and spatial distribution pattern of soils attributes and corn yield in no-tillage system

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

Dolomite and phosphogypsum surface application effects on annual crops nutrition and yield

Brazil has extensive area with acid soils. Using phosphogypsum and soil acidity tolerant cultivars are alternatives to crop establishment in no-till system without previous limestone incorporation in many agricultural soils of Brazil. However, it remains unknown how phosphogypsum and limestone surface application affects rice (Oryza sativa L.) and common bean (Phaseolus vulgaris L.) nutrition and yield under a no-till system. A field experiment was conducted in a sandy clay loam, kaolinitic, thermic Typic Haplorthox, previously cultivated under conventional tillage, in Botucatu, Sao, Paulo State, Brazil. Treatments included four dolomitic limestone rates (0, 1100, 2700, and 4300 kg ha(-1)), two phosphogypsum rates (0 and 2100 kg ha(-1)), and two upland rice cultivars (Caiapo and IAC 202). in 2002-2003, and two bean cultivars (Perola and Carioca), in 2003-2004. Both amendments were applied on the surface, without soil incorporation. The content of Ca, Mg, and Mn in flag leaves and rice yield increased with limestone surface application. Liming increased the shoot dry matter of IAC 202 rice. Phosphogypsum increased S contents in leaves of both rice cultivars, and resulted in higher grain yield in the Caiapo rice. Liming increased K contents in leaves of both bean cultivars. In the absence of phosphogypsum, liming increased S contents and grain yield of bean. Content of Mg in leaves was reduced by phosphogypsum in lower limestone rates. In phosphogypsum presence, liming reduced Zn contents in leaves and increased bean shoot dry matter. Phosphogypsum increased Ca and S, and reduced Mg contents in bean leaves. Using soil acidity tolerant cultivars promoted higher crop yields in no-till systems establishment, even when the effective soil amelioration had not yet been achieved.

Ecological study of Paracoccidioides brasiliensis in soil: growth ability, conidia production and molecular detection

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

Reproductive cycle and recruitment period of Ocypode quadrata (Decapoda, Ocypodidae) at a sandy beach in southeastern Brazil

The reproductive cycle and recruitment period of a ghost crab population from Ubatuba, São Paulo, Brazil were investigated by means of examining the developmental stages of gonads of breeding crabs and the ingress of young recruits to the studied population. Monthly collections over a one-year period were carried out during nocturnal low-tide periods at Vermelha beach. The morphology of the abdomen and pleopods was used for sex determination. All captured crabs were measured for carapace width and dissected for the determination of the development stage of the gonads. A total of 582 specimens was captured: 271 males, 241 females, and 70 juveniles. Size ranged from 8.5 to 37.5 mm for males, from 9.5 to 39.2 mm for females, and from 5.8 to 12 mm for early juveniles. Median size of males and females did not differ statistically. The frequency of ovigerous females was markedly low. The onset of sexual maturity in females is achieved at around 23 mm of carapace width. Mature females with advanced gonad stages were not recorded from May to September. Recruitment of young was highest during summer, but the presence of early and late juvenile specimens throughout the year indicates that continuous recruitment is taking place in the studied population.

Toxicity and Biodegradation in Sandy Soil Contaminated by Lubricant Oils

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

U-ages in soils and groundwater evidencing wet periods 400-600 kyr ago in southeast Brazil

U-238 and its radiogenic daughter U-234 have been utilized for dating soil formation and groundwater residence time during the last 1.5 million years, in this case based on the U-clissolution/precipitation occurring during modifications of the oxidation-reduction conditions. In this paper, we report a 400-600 kyr proxy of wet periods from sediments occurring in a soil profile developed over rocks outcropping at the Parana sedimentary basin in Brazil, and from groundwater exploited of Guarani aquifer at the same basin. The approaches indicated successful use of the U-modeled ages for suggesting wet periods exceeding the past 116-210 kyr from previous studies. (C) 2007 Elsevier Ltd. All rights reserved.

Mercury in soils and sediments from gold mining liabilities in Southern Amazonia

The 1980-1990 Amazonian gold rush left an enormous liability that increasingly has been substituted by developing fish aquaculture. This work aimed at the identification of the mercury levels in the environment, associated with fish farms located in the North of Mato Grosso State, Southern Amazon. Sediment and soil samples were analyzed for total organic carbon and total mercury. Results indicate that the chemical characteristics of the sediment largely depend on the management procedures of the fish pond (liming, fish food used and fish population). The soils presented relatively low concentrations when compared with other data from the literature.