Effect of soil type on burrowing behavior and cocoon formation in the green-striped burrowing frog, Cyclorana alboguttata

This study examined the effect of soil type on burrowing behaviour and cocoon formation during aestivation in the green-striped burrowing frog, Cyclorana alboguttata (Gunther, 1867). Given a choice, frogs always chose to burrow in wet sand in preference to wet clay. Frogs buried themselves faster and dug deeper burrows in sandy soil. However, under my laboratory conditions, there was little difference in the pattern of soil drying between the two soil types. Frogs in both sand and clay soil experienced hydrating conditions for the first 3amonths and dehydrating conditions for the last 3amonths of the 6-month aestivation period, and cocoons were not formed until after 3amonths of aestivation. After 6amonths, there were more layers in the cocoons of frogs aestivating in sand than those aestivating in clay. Frogs were able to absorb water from sandy soil with water potentials greater than -400akPa, but lost water when placed on sand with a water potential of -1000akPa.

Exploring oxidative modifications of tyrosine:an update on mechanisms of formation, advances in analysis and biological consequences

Protein oxidation is increasingly recognised as an important modulator of biochemical pathways controlling both physiological and pathological processes. While much attention has focused on cysteine modifications in reversible redox signalling, there is increasing evidence that other protein residues are oxidised in vivo with impact on cellular homeostasis and redox signalling pathways. A notable example is tyrosine, which can undergo a number of oxidative post-translational modifications to form 3-hydroxy-tyrosine, tyrosine crosslinks, 3-nitrotyrosine and halogenated tyrosine, with different effects on cellular functions. Tyrosine oxidation has been studied extensively in vitro, and this has generated detailed information about the molecular mechanisms that may occur in vivo. An important aspect of studying tyrosine oxidation both in vitro and in biological systems is the ability to monitor the formation of oxidised derivatives, which depends on a variety of analytical techniques. While antibody-dependent techniques such as ELISAs are commonly used, these have limitations, and more specific assays based on spectroscopic or spectrometric techniques are required to provide information on the exact residues modified and the nature of the modification. These approaches have helped understanding of the consequences of tyrosine oxidation in biological systems, especially its effects on cell signalling and cell dysfunction, linking to roles in disease. There is mounting evidence that tyrosine oxidation processes are important in vivo and can contribute to cellular pathology.

Enhanced Growth of Tetracycline-susceptible Soil Bacteria Treated with Iron and Oxytetracycline

Antibiotic resistance has become an important area of research because of the excessive use of antibiotics in clinical and agricultural settings that are driving the evolution of antibiotic resistant bacteria. However, drug tolerance is a naturally occurring phenomenon in soil communities, and is often linked to those soils that are exposed to heavy metals as well as antibiotics. Resistance to antibiotics maybe coupled with resistance to heavy metals in soil bacteria through efflux pumps that can be regulated by iron. Although considered s a heavy metal, iron is an essential component of life that regulates gene expression through the Ferric Uptake Regulator (Fur) protein. This master regulator protein is known to control siderophore production, and other biological pathways. As a suspected controller of biofilm formation, the role of Fur in environmental antibiotic resistance may be greater than is currently realized. In this study, we sought to explore a potential Fur-regulated drug tolerance pathway by understanding the response of soil bacteria when stressed with oxytetracycline and iron. Bacteria were collected from two locations in Miami Dade County. Isolates were first tested using Kirby-Bauer Disk Diffusion tests for antibiotic resistance/susceptibility and identified by 16S rDNA sequencing. A 96-well growth assay was developed to measure planktonic cell growth with 3 mM FeCl3, Oxytetracycline HCl, and the combination treatments. A Microtiter Dish Biofilm Formation Assay was employed and Fur diversity was evaluated. Tetracycline-susceptible bacterial isolates developed drug resistance with iron supplementation, but iron did not enhance biofilm formation. Development of a Fur-dependent drug resistance may be selected for, but further study is required to evaluate Fur evolution in the studied isolates. Gene expression analysis is also needed to further understand the ecological role of Fur and antibiotic resistance.

Glycosylation and Glycodiversification in Polyketide Antibiotics: Unraveling Biosynthetic Steps in Nogalamycin Formation

Soil-dwelling Streptomyces bacteria are known for their ability to produce biologically active compounds such as antimicrobial, immunosuppressant, antifungal and anticancer drugs. S. nogalater is the producer of nogalamycin, a potential anticancer drug exhibiting high cytotoxicity and activity against human topoisomerases I and II. Nogalamycin is an anthracycline polyketide comprising a four-ring aromatic backbone,a neutral deoxy sugar at C7, and an amino sugar attached via an O–C bond at C1 and a C–C bond between C2 and C5´´. This kind of attachment of the amino sugar is unusual thus making the structure of the compound highly interesting. The sugar is also associated with the biological activity of nogalamycin, as it facilitates binding to DNA. Furthermore, the sugar moieties of anthracyclines are often crucial for their biological activity. Together the interesting attachment of the amino sugar and the general reliance of polyketides on the sugar moieties for bioactivity have made the study of the biosynthesis of nogalamycin attractive. The sugar moieties are typically attached by glycosyltransferases, which use two substrates: the donor and the acceptor. The literature review of the thesis is focused on the glycosylation of polyketides and the possibilities to alter their glycosylation patterns. My own thesis work revolves around the biosynthesis of nogalamycin. We have elucidated the individual steps that lead to its rather unique structure. We reconstructed the whole biosynthetic pathway in the heterologous host S. albus using a cosmid and a plasmid. In the process, we were able to isolate new compounds when the cosmid, which contains the majority of the nogalamycin gene cluster, was expressed alone in the heterologous host. The new compounds included true intermediates of the pathway as well as metabolites, which were most likely altered by the endogenous enzymes of the host. The biological activity of the most interesting new products was tested against human topoisomerases I and II, and they were found to exhibit such activities. The heterologous expression system facilitated the generation of mutants with inactivated biosynthetic genes. In that process, we were able to identify the functions of the glycosyltransferases SnogE and SnogD, solve the structure of SnogD, discover a novel C1-hydroxylase system comprising SnoaW and SnoaL2, and establish that the two homologous non-heme α-ketoglutarate and Fe2+ dependent enzymes SnoK and SnoN catalyze atypical reactions on the pathway. We demonstrated that SnoK was responsible for the formation of the additional C–C bond, whereas SnoN is an epimerase. A combination of in vivo and in vitro techniques was utilized to unravel the details of these enzymes. Protein crystallography gave us an important means to understand the mechanisms. Furthermore, the solved structures serve as platforms for future rational design of the enzymes.

Impact of HydroPolymers on the soil biological components in mediterranean drylands

Soil degradation affects more than 52 million ha of land in counties of the European Union. This problem is particularly serious in Mediterranean areas, where the effects of anthropogenic activities (tillage on slopes, deforestation, and pasture production) add to problems caused by prolonged periods of drought and intense and irregular rainfall. Soil microbiota can be used as an indicator of the soil healthy in degraded areas. This is because soil microbiota participates in the cycle elements and in the organic matter decomposition. All this helps to the young plants establishment and in long term protect the soils against the erosion. During dry periods in the Mediterranean areas, the lack of water entering the soil matrix leads to a loss of soil microbiological activity and it turns into a lower soil production capabilities. Under these conditions, the aim of this study was to evaluate the positive effect on soil biological components produced by an hydro absorbent polymer (Terracottem). The aim of the experiment was to evaluate the impact assessment of an hydropolymer (Terracottem) on the soil biological components. An experimental flowerpot layout was established in June 2015 and 12 variants with different amount of Terracottem were applied as follow: i) 3.0 kg.m3 ; ii) 1.5 kg.m3 and; iii) 0 kg.m3. In all the variants were tested the further additives: a) 1% of glucose, b) 50 kg N.ha-1 of Mineral nitrogen, c) 1% of Glucose + 50 kg N.ha-1 of Mineral nitrogen d) control (no additive). According to natural conditions, humidity have been kept at 15% in all the variants. During four weeks, mineral nitrogen leaching and soil respiration have been measured in each flowerplot. Respiration has been quantified four times every time while moistening containers and alkaline soda lime has been used as a sorbent. The amount of CO 2 increase has been measured with the sorbent. Leaching of mineral nitrogen has been quantified by ion exchange resins (IER). IER pouches have been placed on the bottom of each container, and after completion of the experiment mineral nitrogen leaching has been evaluated by distillation and titration method. Results from respiration have shown statistically significant differences between the variants. According to control, soil with polymers have shown significant difference when comparing respiration with independence of the additive used. CO 2 production in the first week has exceeded the sum of the outputs of the following weeks. Mineral nitrogen leaching measurement has shown statistically significant differences. The lowest leaching has been occurred in control variant, while the highest in variant containing only the addition of mineral nitrogen. Research results may conclude that the biological part of the test soil is not limited by a lack of components, the only thing that suppresses its activity is the lack of moisture. After moistening it leads to a rapid growth of soil activity, without causing the nutrients loss. Besides, Terracottem has affected soil activity neither positively nor negatively, but it considers being a suitable tool for reducing the drought impact in arid and semi-arid areas.

Changes In The Bacterial Community Of Soil From A Neutral Mine Drainage Channel.

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments.

Ecdysteroid-Dependent Expression of the Tweedle and Peroxidase Genes during Adult Cuticle Formation in the Honey Bee, Apis mellifera

Cuticle renewal is a complex biological process that depends on the cross talk between hormone levels and gene expression. This study characterized the expression of two genes encoding cuticle proteins sharing the four conserved amino acid blocks of the Tweedle family, AmelTwdl1 and AmelTwdl2, and a gene encoding a cuticle peroxidase containing the Animal haem peroxidase domain, Ampxd, in the honey bee. Gene sequencing and annotation validated the formerly predicted tweedle genes, and revealed a novel gene, Ampxd, in the honey bee genome. Expression of these genes was studied in the context of the ecdysteroid-coordinated pupal-to-adult molt, and in different tissues. Higher transcript levels were detected in the integument after the ecdysteroid peak that induces apolysis, coinciding with the synthesis and deposition of the adult exoskeleton and its early differentiation. The effect of this hormone was confirmed in vivo by tying a ligature between the thorax and abdomen of early pupae to prevent the abdominal integument from coming in contact with ecdysteroids released from the prothoracic gland. This procedure impaired the natural increase in transcript levels in the abdominal integument. Both tweedle genes were expressed at higher levels in the empty gut than in the thoracic integument and trachea of pharate adults. In contrast, Ampxd transcripts were found in higher levels in the thoracic integument and trachea than in the gut. Together, the data strongly suggest that these three genes play roles in ecdysteroid-dependent exoskeleton construction and differentiation and also point to a possible role for the two tweedle genes in the formation of the cuticle (peritrophic membrane) that internally lines the gut.

A possible role of ground-based microorganisms on cloud formation in the atmosphere

The formation of clouds is an important process for the atmosphere, the hydrological cycle, and climate, but some aspects of it are not completely understood. In this work, we show that microorganisms might affect cloud formation without leaving the Earth's surface by releasing biological surfactants (or biosurfactants) in the environment, that make their way into atmospheric aerosols and could significantly enhance their activation into cloud droplets. In the first part of this work, the cloud-nucleating efficiency of standard biosurfactants was characterized and found to be better than that of any aerosol material studied so far, including inorganic salts. These results identify molecular structures that give organic compounds exceptional cloud-nucleating properties. In the second part, atmospheric aerosols were sampled at different locations: a temperate coastal site, a marine site, a temperate forest, and a tropical forest. Their surface tension was measured and found to be below 30 mN/m, the lowest reported for aerosols, to our knowledge. This very low surface tension was attributed to the presence of biosurfactants, the only natural substances able to reach to such low values. The presence of strong microbial surfactants in aerosols would be consistent with the organic fractions of exceptional cloud-nucleating efficiency recently found in aerosols, and with the correlations between algae bloom and cloud cover reported in the Southern Ocean. The results of this work also suggest that biosurfactants might be common in aerosols and thus of global relevance. If this is confirmed, a new role for microorganisms on the atmosphere and climate could be identified.

Time correlation function in systems with two coexisting biological species

We study a stochastic lattice model describing the dynamics of coexistence of two interacting biological species. The model comprehends the local processes of birth, death, and diffusion of individuals of each species and is grounded on interaction of the predator-prey type. The species coexistence can be of two types: With self-sustained coupled time oscillations of population densities and without oscillations. We perform numerical simulations of the model on a square lattice and analyze the temporal behavior of each species by computing the time correlation functions as well as the spectral densities. This analysis provides an appropriate characterization of the different types of coexistence. It is also used to examine linked population cycles in nature and in experiment.

Soil Carbon Turnover Measurement by Physical Fractionation at a Forest-to-Pasture Chronosequence in the Brazilian Amazon

The effect of conversion from forest-to-pasture upon soil carbon stocks has been intensively discussed, but few studies focus on how this land-use change affects carbon (C) distribution across soil fractions in the Amazon basin. We investigated this in the 20 cm depth along a chronosequence of sites from native forest to three successively older pastures. We performed a physicochemical fractionation of bulk soil samples to better understand the mechanisms by which soil C is stabilized and evaluate the contribution of each C fraction to total soil C. Additionally, we used a two-pool model to estimate the mean residence time (MRT) for the slow and active pool C in each fraction. Soil C increased with conversion from forest-to-pasture in the particulate organic matter (> 250 mu m), microaggregate (53-250 mu m), and d-clay (< 2 mu m) fractions. The microaggregate comprised the highest soil C content after the conversion from forest-to-pasture. The C content of the d-silt fraction decreased with time since conversion to pasture. Forest-derived C remained in all fractions with the highest concentration in the finest fractions, with the largest proportion of forest-derived soil C associated with clay minerals. Results from this work indicate that microaggregate formation is sensitive to changes in management and might serve as an indicator for management-induced soil carbon changes, and the soil C changes in the fractions are dependent on soil texture.

Brassinosteroids interact negatively with jasmonates in the formation of anti-herbivory traits in tomato

Given the susceptibility of tomato plants to pests, the aim of the present study was to understand how hormones are involved in the formation of tomato natural defences against insect herbivory. Tomato hormone mutants, previously introgressed into the same genetic background of reference, were screened for alterations in trichome densities and allelochemical content. Ethylene, gibberellin, and auxin mutants indirectly showed alteration in trichome density, through effects on epidermal cell area. However, brassinosteroids (BRs) and jasmonates (JAs) directly affected trichome density and allelochemical content, and in an opposite fashion. The BR-deficient mutant dpy showed enhanced pubescence, zingiberene biosynthesis, and proteinase inhibitor expression; the opposite was observed for the JA-insensitive jai1-1 mutant. The dpyxjai1-1 double mutant showed that jai1-1 is epistatic to dpy, indicating that BR acts upstream of the JA signalling pathway. Herbivory tests with the poliphagous insect Spodoptera frugiperda and the tomato pest Tuta absoluta clearly confirmed the importance of the JA-BR interaction in defence against herbivory. The study underscores the importance of hormonal interactions on relevant agricultural traits and raises a novel biological mechanism in tomato that may differ from the BR and JA interaction already suggested for Arabidopsis.

Carbon and Nitrogen Dynamics in an Oxisol as Affected by Liming and Crop Residues under No-Till

The short-term effects of surface lime application and black oat (Avena strigosa Schreb.) residues, with or without N fertilization, were evaluated in a long-term no-till (NT) system on a sandy clay loam, a kaolinitic, thermic Typic Hapludox from the state of Parana, Brazil. The main plot treatments were: control and dolomitic lime applied on soil surface at 8 Mg ha(-1). Three treatments with crop residues were evaluated on the subplots: (i) fallow, (ii) black oat residues, and (iii) black oat residues aft er N fertilization at 180 kg ha(-1). Black oat dry biomass was not affected by the treatments during 3 yr. Surface liming increased soil pH, microbial biomass, microbial activity, and bacterial/fungal ratio at the soil surface (0-5 cm), resulting in increased amino acid turnover, water-soluble humic substances formation, and N mineralization and nitrification. While the application of black oat did increase the soil pH, overall it had much less effect on soil biological processes and C and N pools than did lime. We concluded that black oat cannot replace the need for lime to optimize crop production in these tropical NT systems. In the long term, however, black oat should aid in the amelioration of acidity and replenishment of soil organic C pools and should help reduce erosion. Overall, this study suggests that overapplication of inorganic fertilizer N may occur in some tropical NT systems. Further experiments are required in NT systems to investigate the use of slow-release N fertilizers in combination with lime and black oat as a mechanism to reduce acidification and promote sustainability.

Using Imaging Spectroscopy to study soil properties

Imaging Spectroscopy (IS) is a promising tool for studying soil properties in large spatial domains. Going from point to image spectrometry is not only a journey from micro to macro scales, but also a long stage where problems such as dealing with data having a low signal-to-noise level, contamination of the atmosphere, large data sets, the BRDF effect and more are often encountered. In this paper we provide an up-to-date overview of some of the case studies that have used IS technology for soil science applications. Besides a brief discussion on the advantages and disadvantages of IS for studying soils, the following cases are comprehensively discussed: soil degradation (salinity, erosion, and deposition), soil mapping and classification, soil genesis and formation, soil contamination, soil water content, and soil swelling. We review these case studies and suggest that the 15 data be provided to the end-users as real reflectance and not as raw data and with better signal-to-noise ratios than presently exist. This is because converting the raw data into reflectance is a complicated stage that requires experience, knowledge, and specific infrastructures not available to many users, whereas quantitative spectral models require good quality data. These limitations serve as a barrier that impedes potential end-users, inhibiting researchers from trying this technique for their needs. The paper ends with a general call to the soil science audience to extend the utilization of the IS technique, and it provides some ideas on how to propel this technology forward to enable its widespread adoption in order to achieve a breakthrough in the field of soil science and remote sensing. (C) 2009 Elsevier Inc. All rights reserved.

Changes in the genetic structure of Bacteria and microbial activity in an agricultural soil amended with tannery sludge

The application of tannery sludge to soils is a form of recycling; however, few studies have examined the impacts of this practice on soil microbial properties. We studied effects of two applications (2006 and 2007) of tannery sludge (with a low chromium content) on the structure of the bacterial community and on the microbial activity of soils. We fertilized an agricultural area in Rolandia, Parana state, Brazil with different doses of sludge based on total N content, which ranged from 0 to 1200 kg N ha(-1). Sludge remained on the soil surface for three months before being plowed. Soils were sampled seven times during the experiment. Bacterial community structure, assessed by denaturing gradient gel electrophoresis (DGGE), was modified by the application of tannery sludge. Soon after the first application, there was clear separation between the bacterial communities in different treatments, such that each dose of sludge was associated with a specific community. These differences remained until 300 days after application and also after the second sludge application, but 666 days after the beginning of the experiment no differences were found in the bacterial communities of the lowest doses and the control. The principal response curve (PRC) analysis showed that the first sludge application strongly stimulated biological activity even 300 days after application. The second application also stimulated activity, but at a lower magnitude and for a shorter time, given that 260 days after the second application there was no difference in biological activity among treatments. PRC also showed that the properties most influenced by the application of tannery sludge were enzymatic activities related to N cycling (asparaginase and urease). The redundancy analysis (RDA) showed that tannery sludge`s influence on microbial activity is mainly related to increases in inorganic N and soil pH. Results showed that changes in the structure of the bacterial community in the studied soils were directly related to changes of their biological activity. (C) 2010 Elsevier Ltd. All rights reserved.

Bacterial communities and biogeochemical transformations of iron and sulfur in a high saltmarsh soil profile

Microbial community structure in saltmarsh soils is stratified by depth and availability of electron acceptors for respiration. However, the majority of the microbial species that are involved in the biogeochemical transformations of iron (Fe) and sulfur (S) in such environments are not known. Here we examined the structure of bacterial communities in a high saltmarsh soil profile and discuss their potential relationship with the geochemistry of Fe and S. Our data showed that the soil horizons Ag (oxic-suboxic), Bg (suboxic), Cri (anoxic with low concentration of pyrite Fe) and Cr-2 (anoxic with high concentrations of pyrite Fe) have distinct geochemical and microbiological characteristics. In general, total S concentration increased with depth and was correlated with the presence of pyrite Fe. Soluble + exchangable-Fe, pyrite Fe and acid volatile sulfide Fe concentrations also increased with depth, whereas ascorbate extractable-Fe concentrations decreased. The occurrence of reduced forms of Fe in the horizon Ag and oxidized Fe in horizon Cr-2 suggests that the typical redox zonation, common to several marine sediments, does not occur in the saltmarsh soil profile studied. Overall, the bacterial community structure in the horizon Ag and Cr-2 shared low levels of similarity, as compared to their adjacent horizons, Bg and Cr-1, respectively. The phylogenetic analyses of bacterial 16S rRNA gene sequences from clone libraries showed that the predominant phylotypes in horizon Ag were related to Alphaproteobacteria and Bacteroidetes. In contrast, the most abundant phylotypes in horizon Cr-2 were related to Deltaproteo-bacteria, Chloroflexi, Deferribacteres and Nitrospira. The high frequency of sequences with low levels of similarity to known bacterial species in horizons Ag and Cr-2 indicates that the bacterial communities in both horizons are dominated by novel bacterial species. (c) 2008 Elsevier Ltd. All rights reserved.