The ecoresponsive genome of Daphnia pulex

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.     

Horticultural performance of ‘Folha Murcha’ sweet orange onto twelve rootstocks

Despite its outstanding position, the Brazilian citriculture is established on a very limited pool of varieties that limits its expansion and restricts the fruit availability throughout the year. This situation determines the urgent necessity of developing alternative scion and rootstock cultivars, with good performance under local conditions. ‘Folha Murcha’ sweet orange (Citrus sinensis (L.) Osbeck) is a late-harvest cultivar, suitable both for the juice processing industry and the fresh fruit market, being described as tolerant to citrus canker (Xanthomonas citri subsp. citri Schaad et al.), and less affected by citrus variegated chlorosis (Xylella fastidiosa Wells et al.). A study was conducted in Bebedouro, São Paulo State, Brazil, to evaluate the horticultural performance of ‘Folha Murcha’ sweet orange budded onto 12 rootstocks: the citrandarin ‘Changsha’ mandarin (Citrus reticulata Blanco) × Poncirus trifoliata ‘English Small’; the hybrid ‘Rangpur’ lime (Citrus limonia Osbeck) × ‘Swingle’ citrumelo (P. trifoliata (L.) Raf. × Citrus paradisi Macfad.); the trifoliates (P. trifoliata (L.) Raf.) ‘Rubidoux’, ‘FCAV’, and ‘Flying Dragon’ (P. trifoliata var. monstrosa); the ‘Sun Chu Sha Kat’ mandarin (C. reticulata Blanco); the ‘Sunki’ mandarin (Citrus sunki (Hayata) Hort. ex. Tanaka); the ‘Rangpur’ limes (C. limonia Osbeck) ‘Cravo Limeira’ and ‘Cravo FCAV’; ‘Carrizo’ citrange (C. sinensis × P. trifoliata), ‘Swingle’ citrumelo (P. trifoliata × C. paradisi), and ‘Orlando’ tangelo (C. paradisi × Citrus tangerina cv. ‘Dancy’). The experimental grove was planted in 2001, using a 7 m × 4 m spacing, in a randomized block design, with five replications and two plants per plot. No supplementary irrigation was applied. Fruit yield, canopy volume, tree tolerance to drought and to citrus variegated chlorosis, and fruit quality were assessed for each rootstock. Trees grafted onto the ‘Flying Dragon’ trifoliate were smaller in size, but had largest yield efficiency when compared to those grafted onto other rootstocks. Lower alternate bearing index was observed on trees budded onto ‘Cravo FCAV’ ‘Rangpur’ lime. Both ‘Rangpur’ lime rootstocks and the ‘Sunki’ mandarin induced higher tree tolerance to drought. The ‘Flying Dragon’ trifoliate induced better fruit quality and higher tolerance to citrus variegated chlorosis (CVC) to ‘Folha Murcha’ trees. A cluster multivariate analysis identified three groups of rootstocks with similar effects on ‘Folha Murcha’ tree performance. Among the 12 evaluated rootstocks, the ‘Flying Dragon’ trifoliate has a unique effect on plant growth, tolerance to drought and CVC, fruit yield and fruit quality of ‘Folha Murcha’ trees, and may be better suited for high-density plantings.     

Spatio-temporal impacts of roads on the persistence of populations: analytic and numerical approaches

Roads can have drastic impacts on wildlife populations. Although there is wide recognition of the negative impacts caused by roads and a wealth of practical studies, there is a lack of theoretical work that can be used to predict the impact of road networks or to implement mitigation measures. Here, using Skellam’s diffusion model, we develop analytic and numerical approaches to analyze the impact of road networks on the survival of populations. Our models show that the viability of a population is determined not only by road density but also by the size and shape of patches. Accordingly, we studied the minimum size of a patch to sustain a population with given diffusion and growth parameters. We provide simple formulas to estimate the minimum patch size, and illustrate the importance of shape with square and rectangular patches. Our models also allow the estimation of time to extinction after road construction for a population in a patch smaller than that of the minimum size. Finally, using numerical computations we illustrate how the spatial arrangement of fences strongly affects both the equilibrium density and the spatial distribution of populations, and that not all fence layouts are equally effective. We anticipate that our methods provide a tool to assess the impact of geometrical features of road networks on wildlife and that they can be used to design mitigation measures to prevent the decline and extinction of populations in an anthropogenically disturbed landscape.     

Effect of a new thermal treatment in combination with saprobic fungal incubation on the phytotoxicity level of alperujo

Byproducts generated from food industries, such as olive oil mills, have been studied to decrease harmful pollution and their environmental consequences. In this work, a new thermal pretreatment and saprobic fungal incubation to detoxify alperujo (two-phase olive mill waste) have been evaluated in view of its use as fertilizer in agriculture. The sequential use of both methods simplifies the thermal conditions and incubation times of the fungal treatment. Optimization of the thermal treatment from 150 to 170 °C for 45 and 15 min, respectively, reduced the incubation time with Coriolpsis rigida from 20 to 10 weeks needed to reduce phytotoxic effects on tomato plants. Therefore, the combination of thermal and biological treatments will allow the development of the potential benefits of alperujo to improve nutrients in agricultural soil.     

Classification of pumpkin seed oils according to their species and genetic variety by attenuated total reflection Fourier-transform infrared spectroscopy

Attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR), followed by multivariate treatment of the spectral data, was used to classify seed oils of the genus Cucurbita (pumpkins) according to their species as C. maxima, C. pepo, and C. moschata. Also, C. moschata seed oils were classified according to their genetic variety as RG, Inivit C-88, and Inivit C-2000. Up to 23 wavelength regions were selected on the spectra, each region corresponding to a peak or shoulder. The normalized absorbance peak areas within these regions were used as predictors. Using linear discriminant analysis (LDA), an excellent resolution among all categories concerning both Cucurbita species and C. moschata varieties was achieved. The proposed method was straightforward and quick and can be easily implemented. Quality control of pumpkin seed oils is important because Cucurbita species and genetic variety are both related to the pharmaceutical properties of the oils.     

Fermented vegetables containing benzoic and ascorbic acids as additives: benzene formation during storage and impact of additives on quality parameters

Chemical and sensorial changes related to the use of benzoates and ascorbic acid as additives in packed fermented vegetables were investigated. For this, three selected vegetables (green olives, cucumbers, and caperberries) stored under different conditions (glass or plastic containers, ambient or refrigerated storage) were used. In all cases, benzoic acid remained unchanged (glass bottle) or decreased slightly (plastic pouch) at prolonged storage. Ascorbic acid was partially or totally degraded during storage, the degradation rate depending on the storage conditions and the vegetable matrix. Benzene levels higher than 10 μg/L were found in cucumbers and caperberries containing both additives, but only when packed in plastic pouches and after prolonged storage at room temperature. In these conditions, an appreciable browning of brine, related to AA degradation, was also found. The use of benzoate alone had a significant influence on vegetable color, but flavor was not significantly affected at the benzoate levels tested. On the basis of the present study, benzoates should be removed from fermented vegetable formulations containing ascorbic acid to eliminate possible benzene formation during long-term storage.     

Influence of the soil/solution ratio, interaction time, and extractant on the evaluation of iron chelate sorption/desorption by soils

Synthetic Fe chelates are the most efficient agricultural practice to control Fe deficiency in crops, EDTA/Fe3+ and o,o-EDDHA/Fe3+ being the most commonly used. Their efficacy as Fe sources and carriers in soils can be severely limited by their retention on it. The aim of this work is to evaluate the possible bias introduced in the studies of the iron chelate retention by soils. For that purpose, results obtained for EDTA and EDDHA iron chelates from two batch studies with different soil/solution ratios were compared with data obtained for a leaching column experiment. Moreover, different extractants were tested to study the o,o-EDDHA/Fe3+ and o,p-EDDHA/Fe3+ desorption from a calcareous soil, and also the effect of the interaction time in their retention process has been evaluated. In summary, the mobility through a calcareous soil of the studied iron chelates differs greatly depending on the type of iron chelate and also on the procedure used to evaluate the retention and the soil/solution ratio used. In general, the leaching column method is preferred because the achieved conclusions are more representative of the natural conditions, but batch methods are very useful as a preliminary experiment, especially one with a high soil/solution ratio. The iron chelate desorption could be quantified by using a sequential extraction with water, sodium sulfate, and DTPA as extractants. Under the experimental conditions used in this study, o,o-EDDHA/Fe3+ retention increased with interaction time.     

Profiling LC-DAD-ESI-TOF MS method for the determination of phenolic metabolites from avocado (Persea americana)

A powerful HPLC-DAD-ESI-TOF MS method was established for the efficient identification of the chemical constituents in the methanolic extracts of avocado (Persea americana). Separation and detection conditions were optimized by using a standard mix containing 39 compounds belonging to phenolic acids and different categories of flavonoids, analytes that could be potentially present in the avocado extracts. Optimum LC separation was achieved on a Zorbax Eclipse Plus C18 analytical column (4.6×150 mm, 1.8 μm particle size) by gradient elution with water+acetic acid (0.5%) and acetonitrile as mobile phases, at a flow rate of 1.6 mL/min. The detection was carried out by ultraviolet-visible absorption and ESI-TOF MS. The developed method was applied to the study of 3 different varieties of avocado, and 17 compounds were unequivocally identified with standards. Moreover, around 25 analytes were tentatively identified by taking into account the accuracy and isotopic information provided by TOF MS.     

Soil variability through spatial scales in a permanently disturbed natural spruce-fir-beech forest

Soil variability was assessed in a 74.2-ha area within the Žofínsky prales natural forest. Parameters evaluated for 1765 soil profiles inside 353 graticule plots were as follows: (1) thickness of organic horizons, (2) thickness and form of mineral horizons, (3) humus form (HF), (4) soil taxonomic unit (STU) and (5) anomalies. In addition, soil reaction (pH_KCl) and oxidizable carbon content (C_ox) were measured in the laboratory for 734 samples from the upper mineral (A) and lower mineral (B) horizons. The most frequently occurring humus form was mor followed by moder, hydromor and peaty T-horizon. Entic Podzols, Dystric Cambisols, Haplic Cambisols, Albic Podzols, Histic (or Haplic) Gleysols, Endogleyic Stagnosols, Fibric or Hemic or Sapric Histosols and Stagnic Gleysols were all present at the site despite its homogeneous geological bedrock. Overall coefficient of variance (CV) was lower in terrestrial soils compared with (semi-)hydromorphic soils. Overall variance decreased in both soil groups with increasing depth, as did CV differences between the fine (up to 10 m) and the locality scales. The lowest CV values occurred for C_ox and pH_KCl. The CV values differed between STUs as well. Compared to lower horizons, variograms of upper horizons showed greater autocorrelation at the intermediate spatial scale (10–320 m)—ranging from 50 to 150 m. Semivariance values, however, reached 70–80% of sill already at a distance of 10 m. The most significant factor of variability at all studied spatial scales is presumably the soil disturbance regime, followed by terrain micro-topography and the effect of tree species.     

Do mature pine plantations resemble deciduous natural forests regarding understory plant diversity and canopy structure in historically modified landscapes?

We compared the structure of the arboreal layer and the diversity and species composition of the understory vegetation of three types of mature forest communities: oak (Quercus pyrenaica) and beech (Fagus sylvatica) forests and Scots pine (Pinus sylvestris) plantations. Our main aim was to determine whether differences in these variables existed and were due to the identity of the dominant tree species. We selected four stands or replicates per forest type located geographically close and with relatively similar conditions. We found no differences in the arboreal structure of oak and beech forests, which were characterised by great variability in tree size, while in case of plantations, this variability was lower at both the intra-stand (estimated by the coefficient of variation) and inter-stand (i.e. the four replicates harboured trees of similar sizes) scales. However, the highest variability in the canopy layer of natural forests was not consistently linked to greater understory species richness. Indeed, the lowest plant species richness was found in beech forests, while oak forests harboured the highest value at either the sampling unit (per m²) or stand scales. The greatest negative correlation between plant diversity and the environmental variables measured was found for litter depth, which was the highest in beech forests. The results obtained by the CCA indicated that the four replicates of each forest type clustered together, due to the presence of characteristic species. We concluded that pine plantations did not approach the environmental conditions of native forests, as plantations were characterised by singular understory species composition and low arboreal layer variability, compared to natural woodlands.