Glycoprofiling of bifidobacterial consumption of human milk oligosaccharides demonstrates strain specific, preferential consumption of small chain glycans secreted in early human lactation

The molecular basis by which human breast milk supports the development of a protective intestinal microbiome in infants is unknown. After lactose and lipids, human milk oligosaccharides (HMOs) are quantitatively the third largest and most diverse component of breast milk. In this work, glycomic profiling of HMO consumption by bifidobacteria using Fourier transform ion cyclotron resonance mass spectrometry reveals that one species, Bifidobacterium longum biovar infantis ATCC 15697, an isolate from the infant gut, preferentially consumes small mass oligosaccharides, representing 63.9% of the total HMOs available. These HMOs were detected in human breast milk at the onset and constantly through the first month of lactation by use of high performance liquid chromatography-chip time-of-flight mass spectrometry. Further characterization revealed that strain ATCC 15697 possesses both fucosidase and sialidase activities not present in the other tested strains. This work provides evidence that these small mass HMOs are selectively metabolized by select bifidobacterial strains and represent a potential new class of bioactive molecules functioning as prebiotics to facilitate a protective gut colonization in breast-fed newborns.     

Root colonisation by arbuscular mycorrhizal, fine endophytic and dark septate fungi across a pH gradient in acid beech forests

Colonisation by root endophytes can be beneficial to plants growing on acid, nutrient-poor soils. Arbuscular mycorrhizal (AM) fungi can supply herbs with nutrients and may give protection against aluminium toxicity. Two other root colonising fungi, fine endophytes (FE) and dark septate fungi (DSE), are less well known but are potentially of benefit to their host plant. AM fungi are the most prevalent symbionts in herbs at neutral to acidic soil pH. At extremely low pH, fungal growth can be limited and AM colonisation is usually rare. Fine and dark septate endophytes, on the other hand, have been observed more often under these conditions. In order to relate endophyte colonisation to a gradient in soil pH, we investigated root colonisation by AM, FE and DSE in Maianthemum bifolium, Galium odoratum, Mercurialis perennis and Stellaria nemorum, from a range of acidic beech forests. With decreasing pH, colonisation by AM decreased, whereas the other two endophytes increased. AM and FE colonisation were inversely correlated in Maianthemum bifolium. We compared changes in root colonisation with those in chemical composition of soil and leaf samples and found a positive correlation between leaf magnesium concentrations and the presence of DSE in Galium odoratum. Aluminium concentration in Maianthemum bifolium tended to be lower when FE colonisation was high, suggesting a possible role for the fungi in plant protection against Al. We suggest that FE and DSE may replace AM fungi in herbaceous vegetation at extremely low pH, counteracting some of the negative effects of high soil acidity on plants.     

Soil colloids-bound plasmid DNA: Effect on transformation of E. coli and resistance to DNase I degradation

The adsorption and binding of plasmid p34S DNA on four different colloidal fractions from a Brown soil and clay minerals in the presence of various Ca²⁺ concentrations, the ability of bound DNA to transform competent cells of CaCl₂-treated Escherichia coli, and the resistance of bound DNA to degradation by DNase I were studied. DNA adsorption on soil colloids and clay minerals was promoted in the presence of Ca²⁺. Kaolinite exhibited the highest adsorption affinity for DNA among the examined soil colloids and clay minerals. In comparison with organo-mineral complexes (organic clays) and fine clays (<0.2 μm), DNA was tightly adsorbed by H₂O₂-treated clays (inorganic clays) and coarse clays (0.2-2 μm). The transformation efficiency of bound DNA increased with increasing concentrations of Ca²⁺ at which soil colloid or clay mineral-DNA complexes were formed. DNA bound by kaolinite showed the lowest transformation efficiency, and especially no transformants were observed with kaolinite-DNA complex prepared at 5-100 mM Ca²⁺. Compared to organic clays and fine clays, DNA bound on inorganic clays and coarse clays showed a lower capacity to transform E. coli at different Ca²⁺ concentrations. The presence of soil colloids and minerals provided protection to DNA against degradation by DNase I. Montmorillonite, organic clays and fine clays showed stronger protective effects for DNA than inorganic clays and coarse clays. The protection mechanisms as well as the differences in transforming efficiency of plasmid DNA molecules bound on various soil colloidal particles are discussed. The information obtained in this study is of fundamental significance for the understanding of the horizontal dissemination of recombinant DNA and the fate of extracellular DNA in soil environments.     

Changes in chemical and biological properties of a sodic clay subsoil with addition of organic amendments

An experiment was performed to examine the chemical and biological effects on high clay sodic subsoil following the incorporation and incubation with organic amendments. The main treatments consisted of amendments with wheat shoots, lucerne pellets and peat, and these were compared to gypsum addition. Additional treatments were residues of chickpea and canola, chicken manure and sawdust. All materials were finely ground and added to crushed and sieved soil at the rate of 1% by weight. Wheat, canola and chickpea residues and chicken manure resulted in modest reductions in soil sodicity. Carbon and N mineralization were related to the soluble C/total N ratio in the amendment. The initial mineralization of wheat amendment was rapid due to its soluble C content, but then slowed to have the lowest loss, of around one third of added C, of all the plant residues after 174 days. In comparison, lucerne-amended soil increased total N and lost almost half of its C after the 174-day incubation. The canola stubble amendment showed the highest carbon loss, losing 64% of its added C. The addition of gypsum resulted in high soil electrical conductivity which suppressed respiration, compared to the control soil, indicating a detrimental effect on microbial activity due to the high electrolyte concentration in the soil. The peat amendment, with a low-soluble C content, showed a similar respiration rate to the control soil, confirming that a source of soluble C is important for the initiation of rapid biological activity. Soil pH was significantly increased (by 0.6 of a pH unit) with addition of chicken manure, and still remained higher than control soil after 174 days of incubation. Lucerne was the only plant residue to increase soil pH, with the effect being sustained for 56 days. The study demonstrated how some organic amendments can improve chemical fertility and biological activity in high clay sodic subsoil, and at the same time contribute, after 25 weeks incubation, to an increase in carbon content.     

Potential of Borago officinalis, Sinapis alba L. and Phacelia boratus for Phytoextraction of Cd and Pb from Soil

Heavy metal phytoextraction is a soil remediation technique, which makes use of plants in removing contamination from soil. The plants must thus be tolerant to heavy metals, adaptable to soil and climate characteristics, and able to take up large amounts of heavy metals. Most of the high biomass productive plants such as, maize, oat and sunflower are plants, which do not grow in cold climates or need intensive care. In this study three “weed” plants, Borago officinalis; Sinapis alba L. and Phacelia boratus were investigated for their ability to tolerate and accumulate high amounts of Cd and Pb. Pot experiments were performed with soil containing Cd and Pb at concentrations of up to 180 mg kg^?1 and 2,400 mg kg^?1 respectively. All three plants showed high levels of tolerance. Borago officinalis; and Sinapis alba L. accumulated 109 mg kg^?1 and 123 mg kg^?1 Cd, respectively at the highest Cd spiked soil concentration. Phacelia boratus reached a Cd concentration of 42 mg kg^?1 at a Cd soil concentration of 100 mg kg^?1. In the case of Pb, B. officinalis and S. alba L. displayed Pb concentrations of 25 mg kg^?1 and 29 mg kg^?1, respectively at the highest Pb spiked soil concentration. Although the Pb uptake in P. boratus reached up to 57 mg kg^?1 at a Pb spiked soil concentration of 1,200 mg kg^?1, it is not suitable for phytoextraction because of its too low biomass.     

Recovery of cover-crop-N in the soil-plant system in the Guinea savannah zone of Ghana

In order to understand the efficiency of residue-N use and to estimate the minimum input required to obtain a reasonable level of crop response, it is important to quantify the fate of the applied organic-N. The recovery of N from ¹⁵N-labelled Crotalaria juncea was followed in the soil and the succeeding maize crop. Apparent N recovery (ANR) by maize from unlabelled Crotalaria juncea, Crotalaria retusa, Calopogonium mucunoides, Mucuna pruriens and mineral fertilizer at three locations were also evaluated. The maize crop recovered 4.7% and 7.3% of the ¹⁵N-labelled C. juncea-N at 42 days after sowing (DAS) and at final harvest, respectively. The corresponding ¹⁵N recovery from the soil was 92.4% and 58.5%. The highest mean ANR of 57.4% was with mineral fertilizer, whereas the mean ANR of 14.3% from C. retusa was the lowest. A large pool substitution and added-N interaction effect was observed when comparing N recovery from the labelled and unlabelled C. juncea. The amount of residue-N accounted for by the isotope dilution method at 42 DAS was 97.1% and at final harvest 65.8%. The large residue-N recovery in the soil organic-N pool explains the residual effect usually observed with organic residue application.     

Effects of genetically modified plants on microbial communities and processes in soil

The development and use of genetically modified plants (GMPs) has been a topic of considerable public debate in recent years. GMPs hold great promise for improving agricultural output, but the potential for unwanted effects of GMP use is still not fully understood. The majority of studies addressing potential risks of GMP cultivation have addressed only aboveground effects. However, recent methodological advances in soil microbial ecology have allowed research focus to move underground to try to gain knowledge of GMP-driven effects on the microbial communities and processes in soil that are essential to key terrestrial ecosystem functions. This review gives an overview of the research performed to date on this timely topic, highlighting a number of case studies. Although such research has advanced our understanding of this topic, a number of knowledge gaps still prevent full interpretation of results, as highlighted by the failure of most studies to assign a definitively negative, positive or neutral effect to GMP introduction. Based upon our accumulating, yet incomplete, understanding of soil microbes and processes, we propose a synthesis for the case-by-case study of GMP effects, incorporating assessment of the potential plant/ecosystem interactions, accessible and relevant indicators, and tests for unforeseen effects.     

Radical scavenging activity of black cumin (Nigella sativa L.), coriander (Coriandrum sativum L.), and niger (Guizotia abyssinica Cass.) crude seed oils and oil fractions

Crude vegetable oils are usually oxidatively more stable than the corresponding refined oils. Tocopherols, phospholipids (PL), phytosterols, and phenols are the most important natural antioxidants in crude oils. Processing of vegetable oils, moreover, could induce the formation of antioxidants. Black cumin (Nigella sativa L.), coriander (Coriandrum sativum L.), and niger (Guizotia abyssinica Cass.) crude seed oils were extracted with n-hexane and the oils were further fractionated into neutral lipids (NL), glycolipids (GL), and PL. Crude oils and their fractions were investigated for their radical scavenging activity (RSA) toward the stable galvinoxyl radical by electron spin resonance (ESR) spectrometry and toward 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical by spectrophotometric method. Coriander seed oil and its fractions exhibited the strongest RSA compared to black cumin and niger seed oils. The data correlated well with the total content of polyunsaturated fatty acids, unsaponifiables, and PL, as well as the initial peroxide values of crude oils. In overall ranking, RSA of oil fractions showed similar patterns wherein the PL exhibited greater activity to scavenge both free radicals followed by GL and NL, respectively. The positive relationship observed between the RSA of crude oils and their color intensity suggests the Maillard reaction products may have contributed to the RSA of seed oils and their polar fractions. The results demonstrate the importance of minor components in crude seed oils on their oxidative stability, which will reflect on their food value and shelf life. As part of the effort to assess the potential of these seed oils, the information is also of importance in processing and utilizing the crude oils and their byproducts.     

Contamination of pastures by polycyclic aromatic hydrocarbons (PAHs) in the vicinity of a highway

To assess PAH contamination pastures, grass and soil samples have been collected from 10 m (d1), 50 m (d2), and 150 m (d3) perpendicular to a French highway (70,000 vehicles per day) and at a control site in a rural area away from nearby contaminating sources. Total PAH concentration ranges from 767 ng/g dry weight to 3989 ng/g dry weight, according to the matrix and the distance from the highway. Distance is not a significant factor for PAH deposition on grass, while in soil it has an effect between d1 and d2 or d3. The total PAH concentration in highway samples is 8 times higher than in control site samples for grass and 7 to 4 times higher for soil. Fluoranthene, pyrene, and phenanthrene are the major PAHs in grass samples at the control site and the highway, but the concentrations are about 5 times higher near the highway. In soil samples collected near the highway, the values of concentrations between all compounds are not statistically different. PAH deposition on grass is linked to the physicochemical properties of the compounds, which lead to a specific distribution of each molecule (according to their volatility and the number of aromatic rings) while no specific behavior is revealed in soil.