Positive and negative impacts of plants on acid production in exposed acid sulphate soils

This study examined the impact of plants on acid sulphate soils with the aim of determining whether plants are able to reduce acid production. The study was conducted with clayey acid sulphate soil under controlled conditions with treatments lasting up to 24 weeks and measurements made in the top 0?C60 mm of soil. pH profiles in the soil were strongly dependent on soil moisture and the pattern of irrigation. When bare soil was allowed to dry down without further irrigation, there was very little acidification of either the surface or subsurface layers. Planting of Phragmites accelerated soil drying and caused extensive cracking and acidification of the subsoil under simulated drought conditions. Under a wetting and drying regime, both Phragmites and a surface spreading grass Paspalum increased soil acidification, while a surface spreading herbaceous shrub Cotula had little effect on acidification. There was no evidence that live plants could ameliorate acid sulphate soils. However, application of dead plant matter to the surface of the soil was effective in reducing acidification, especially if submerged.     

Reorientation and Dimerization of the Membrane-Bound Antimicrobial Peptide PGLa from Microsecond All-Atom MD Simulations

Platelet spreading is critical for hemostatic plug formation and thrombosis. However, the detailed dynamics of platelet spreading as a function of receptor-ligand adhesive interactions has not been thoroughly investigated. Using reflection interference contrast microscopy, we found that both adhesive interactions and PAR4 activation affect the dynamics of platelet membrane contact formation during spreading. The initial growth of close contact area during spreading was controlled by the combination of different immobilized ligands or PAR4 activation on fibrinogen, whereas the growth of the total area of spreading was independent of adhesion type and PAR4 signaling. We found that filopodia extend to their maximal length and then contract over time; and that filopodial protrusion and expansion were affected by PAR4 signaling. Upon PAR4 activation, the integrin α_IIbβ₃ mediated close contact to fibrinogen substrata and led to the formation of ringlike patterns in the platelet contact zone. A systematic study of platelet spreading of GPVI-, α₂-, or β₃-deficient platelets on collagen or fibrinogen suggests the integrin α₂ is indispensable for spreading on collagen. The platelet collagen receptors GPVI and α₂ regulate integrin α_IIbβ₃-mediated platelet spreading on fibrinogen. This work elucidates quantitatively how receptor-ligand adhesion and biochemical signals synergistically control platelet spreading.     

Effect of colcemid on the spreading of fibroblasts in culture

The effect of colcemid upon the spreading of mouse embryo fibroblast-like cells on substrates was studied with the aid of time-lapse microcinematography and scanning electron microscopy. Two types of substrates were used: flat glass and narrow strips of glass surrounded by non-adhesive lipid film; on the latter, spreading and polarization of cells proceeded simultaneously. On glass, colcemid did not prevent transition of cells into a well-attached state; however, the time required for this transition increased considerably as compared with control cultures. Similar effects were caused by two other drugs inhibiting the formation of microtubules: colchicine and vinblastine. The intermediate stages of spreading on flat glass had several abnormal features in the colcemid-containing medium: (a) the shape of cytoplasmatic outgrowths formed by the cell was altered and their distribution became less regular; (b) partial detachment of the attached parts of the cells was very frequent; (c) the spreading of various parts of the cell was not well correlated: the central part of the cell could remain unspread long after the spreading of the peripheral part. Similar effects of colcemid were observed in experiments with cells spreading on the narrow strips of the glass. In addition, colcemid prevented stabilization of the cell surface, i.e., differentiation of the cellular edge into active and stable parts. About two-thirds of the cells attached to the narrow strips of glass were completely detached from the substrate in the course of spreading in colcemid-containing medium. The possible mechanisms of the action of colcemid on spreading are discussed and it is suggested that intracellular structures sensitive to colcemid are essential for the coordination of the reactions in various parts of the cell in the course of spreading.     

Bacterial diversity in ornithogenic soils compared to mineral soils on King George Island, Antarctica

In the Nar?bski Point area of King George Island of Antarctica, ornithogenic soils form on land under Chinstrap and Gentoo Penguin rookeries. The purpose of this study was to compare the bacterial community compositions in the gradient of contamination by penguin feces; mineral soil with no contamination, and soils with medium or high contamination. The discrimination between mineral soils and ornithogenic soils by characterization of physicochemical properties and bacterial communities was notable. Physicochemical analyses of soil properties showed enrichment of carbon and nitrogen in ornithogenic soils. Firmicutes were present abundantly in active ornithogenic soils, Bacteroidetes and Proteobacteria in a formerly active one, and several diverse phyla such as Proteobacteria, Actinobacteria, and Acidobacteria in mineral soils. Some predominant species belonging to the Firmicutes and Gammaproteobacteria may play an important role for the mineralization of nutrients in ornithogenic soils. Results of this study indicate that dominant species may play an important role in mineralization of nutrients in these ecosystems.     

Nostoc cyanobacterial inoculation in South African agricultural soils enhances soil structure, fertility, and maize growth

Many soils in South Africa have low nutrient supply, poor structural stability and are prone to soil erosion due to susceptibility to surface sealing and crusting. Two crusting soils from the Eastern Cape Province, South Africa were used to evaluate the effects of inoculation with a strain of Nostoc on soil structure, fertility and maize growth. The Nostoc suspension was uniformly applied over potted soils at a rate of 6g (dry weight) per square meter soon after maize germination. Nostoc inoculation increased soil N by 17% and 40% in Hertzog and Guquka soils, respectively. Soil C was also increased significantly and this increase was strongly associated with that of soil N (R ² = 0.838). The highest contents of soil C, soil N and mineral N, however, were found in non-cropped Nostoc inoculated soils. Nostoc inoculation increased maize dry matter yields by 49% and 40% in Hertzog and Guquka soils, respectively. Corresponding increases in maize tissue N were 23% and 14%, respectively. Scanning electron microscopy (SEM) revealed that soil particles and fragments of non-cropped inoculated soils had coatings of extracellular polymeric substances (EPS) with other particles enmeshed in networks of filaments, whilst by contrast little or no EPS and/or filaments were observed on cropped and/or non-inoculated soils. This was consistent with chemical analysis which showed that Nostoc caused significant increases in the EPS and soil C contents of non-cropped soils. The proportion of very stable aggregates was increased by inoculation with Nostoc possibly due to the greater quantities of soil C and EPS observed in inoculated soils. Inoculated soils cropped with maize had a lower proportion of stable aggregates presumably due to their low soil C and EPS contents compared to non-cropped soils. The results suggested that Nostoc could improve the fertility and structural stability of the studied degraded soils.     

A Novel Gene,fudoh, in the SCCmec Region Suppresses the Colony Spreading Ability and Virulence of Staphylococcus aureus

Staphylococcus aureus colonies can spread on soft agar plates. We compared colony spreading of clinically isolated methicillin-sensitive S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA). All MSSA strains showed colony spreading, but most MRSA strains (73%) carrying SCCmec type-II showed little colony spreading. Deletion of the entire SCCmec type-II region from these MRSA strains restored colony spreading. Introduction of a novel gene, fudoh, carried by SCCmec type-II into Newman strain suppressed colony spreading. MRSA strains with high spreading ability (27%) had no fudoh or a point-mutated fudoh that did not suppress colony spreading. The fudoh-transformed Newman strain had decreased exotoxin production and attenuated virulence in mice. Most community-acquired MRSA strains carried SCCmec type-IV, which does not include fudoh, and showed high colony spreading ability. These findings suggest that fudoh in the SCCmec type-II region suppresses colony spreading and exotoxin production, and is involved in S. aureus pathogenesis.     

The Efficacy of Yellow Tape Formulation of Pyriproxyfen against the Sweet Potato Whitefly,Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae)

A tape formulation of pyriproxyfen was prepared by coating the chemical onto yellow plastic film. We evaluated the transovarial ovicidal activity of the tape formulation against Bemisia tabaci and investigated the optimal application method and efficacy in a greenhouse. The tape formulation showed high ovicidal activity of over 80% mortality against B. tabaci for 4 days by a 30-second compulsory contact test. The formulation controlled the B. tabaci population on tomatoes by both “sideways spreading application” and “vertical hanging application”. “Sideways spreading application” was considered to be more practical, although there was no significant difference in efficacy between the two application methods. In a large-scale greenhouse trial of “sideways spreading application”, the tape formulation suppressed the B. tabaci population for 77 days. The results suggested that the tape formulation is promising as a tool for IPM because of its high efficacy and lower environmental impact.     

Age-associated reduction of cell spreading induces mitochondrial DNA common deletion by oxidative stress in human skin dermal fibroblasts: implication for human skin connective tissue aging

Background

Reduced cell spreading is a prominent feature of aged dermal fibroblasts in human skin in vivo. Mitochondrial DNA (mtDNA) common deletion has been reported to play a role in the human aging process, however the relationship between age-related reduced cell spreading and mtDNA common deletion has not yet been reported.

Results

To examine mtDNA common deletion in the dermis of aged human skin, the epidermis was removed from full-thickness human skin samples using cryostat. mtDNA common deletion was significantly elevated in the dermis of both naturally aged and photoaged human skin in vivo. To examine the relationship between age-related reduced cell spreading and mtDNA common deletion, we modulated the shape of dermal fibroblasts by disrupting the actin cytoskeleton. Reduced cell spreading was associated with a higher level of mtDNA common deletion and was also accompanied by elevated levels of endogenous reactive oxygen species (ROS). Boosting cellular antioxidant capacity by using antioxidants was found to be protective against mtDNA common deletion associated with reduced cell spreading.

Conclusion

mtDNA common deletion is highly prevalent in the dermis of both naturally aged and photoaged human skin in vivo. mtDNA common deletion in response to reduced cell spreading is mediated, at least in part, by elevated oxidative stress in human dermal fibroblasts. These data extend current understanding of the mitochondrial theory of aging by identifying the connection between mtDNA common deletion and age-related reduction of cell spreading.     

Biotic and Abiotic Soil Properties Influence Survival of Listeria monocytogenes in Soil

Listeria monocytogenes is a food-borne pathogen responsible for the potentially fatal disease listeriosis and terrestrial ecosystems have been hypothesized to be its natural reservoir. Therefore, identifying the key edaphic factors that influence its survival in soil is critical. We measured the survival of L. monocytogenes in a set of 100 soil samples belonging to the French Soil Quality Monitoring Network. This soil collection is meant to be representative of the pedology and land use of the whole French territory. The population of L. monocytogenes in inoculated microcosms was enumerated by plate count after 7, 14 and 84 days of incubation. Analysis of survival profiles showed that L. monocytogenes was able to survive up to 84 days in 71% of the soils tested, in the other soils (29%) only a short-term survival (up to 7 to 14 days) was observed. Using variance partitioning techniques, we showed that about 65% of the short-term survival ratio of L. monocytogenes in soils was explained by the soil chemical properties, amongst which the basic cation saturation ratio seems to be the main driver. On the other hand, while explaining a lower amount of survival ratio variance (11%), soil texture and especially clay content was the main driver of long-term survival of L. monocytogenes in soils. In order to assess the effect of the endogenous soils microbiota on L. monocytogenes survival, sterilized versus non-sterilized soils microcosms were compared in a subset of 9 soils. We found that the endogenous soil microbiota could limit L. monocytogenes survival especially when soil pH was greater than 7, whereas in acidic soils, survival ratios in sterilized and unsterilized microcosms were not statistically different. These results point out the critical role played by both the endogenous microbiota and the soil physic-chemical properties in determining the survival of L. monocytogenes in soils.     

Soybean Photosynthesis and Yield as Influenced by Heterodera glycines,Soil Type and Irrigation

The effects of soil types and soil water matric pressure on the Heterodera glycines-Glycine max interaction were examined in microplots in 1988 and 1989. Reproduction of H. glycines was restricted in fine-textured soils as compared with coarse-textured ones. Final population densities of this pathogen in both years of the study were greater in nonirrigated soils than in irrigated soils. The net photosynthetic rate of soybean (per unit area of leaf) was suppressed only slightly or not at all in response to infection by H. glycines and other stresses. Relative soybean-yield suppression in response to H. glycines was not affected by water content in fine-textured soils, but slopes of the damage functions were steepest in sand, sandy loam, and muck soils at high water content (irrigated plots). Yield restriction of soybean in response to this pathogen under irrigation was equal to or greater than the yield suppression under dry conditions. Although yield potential may be elevated by irrigation when soil-water content is inadequate, supplemental irrigation cannot be used to circumvent nematode damage to soybean.     

Morpho-Typing and Molecular Diversity of Arbuscular Mycorrhizal Fungi in Sub-Tropical Soils of Coimbatore Region, Tamil Nadu, India

The diversity potential of arbuscular mycorrhizal fungi (AMF) in three different tropical soils of southern part of India was assessed by traditional morpho-typing of AMF-spores and by culture-independent nested-PCR of internal transcribed spacer region of ribosomal genes. The population diversity of AMF in soil was strongly correlated with available P₂O₅ in soil. Among the three different soils, black-cotton soil had more diversified AMF species than alluvial and red sandy soils. Pooled data of morpho-typing and sequence-driven analysis revealed that Glomus, Gigaspora, Scutellospora and Acaulospora are the AMF genera present in these soils. The diversity of AMF in soil differs with the mycorrhiza colonizing the plant roots.     

Interaction of Crk with Myosin-1c Participates in Fibronectin-Induced Cell Spreading

We previously reported a novel interaction between v-Crk and myosin-1c, and demonstrated that this interaction is essential for cell migration, even in the absence of p130CAS. We here demonstrate a role for Crk-myosin-1c interaction in cell adhesion and spreading. Crk-knockout (Crk^‑/‑) mouse embryo fibroblasts (MEFs) exhibited significantly decreased cell spreading and reduced Rac1 activity. A stroboscopic analysis of cell dynamics during cell spreading revealed that the cell-spreading deficiency in Crk^‑/‑ MEFs was due to the short protrusion/retraction distances and long persistence times of membrane extensions. The low activity of Rac1 in Crk^‑/‑ MEFs, which led to delayed cell spreading in these cells, is consistent with the observed defects in membrane dynamics. Reintroduction of v-Crk into Crk^‑/‑ MEFs rescued these defects, restoring cell-spreading activity and membrane dynamics to Crk^+/+ MEF levels, and normalizing Rac1 activity. Knockdown of myosin-1c by introduction of small interfering RNA resulted in a delay in cell spreading and reduced Rac1 activity to low levels, suggesting that myosin-1c also plays an essential role in cell adhesion and spreading. In addition, deletion of the v-Crk SH3 domain, which interacts with the myosin-1c tail, led to defects in cell spreading. Overexpression of the GFP-myosin-1c tail domain effectively inhibited the v-Crk-myosin-1c interaction and led to a slight decrease in cell spreading and cell surface area. Collectively, these findings suggest that the v-Crk-myosin-1c interaction, which modulates membrane dynamics by regulating Rac1 activity, is crucial for cell adhesion and spreading.     

Effect of Afforestation and Reforestation of Pastures on the Activity and Population Dynamics of Methanotrophic Bacteria

We investigated the effect of afforestation and reforestation of pastures on methane oxidation and the methanotrophic communities in soils from three different New Zealand sites. Methane oxidation was measured in soils from two pine (Pinus radiata) forests and one shrubland (mainly Kunzea ericoides var. ericoides) and three adjacent permanent pastures. The methane oxidation rate was consistently higher in the pine forest or shrubland soils than in the adjacent pasture soils. A combination of phospholipid fatty acid (PLFA) and stable isotope probing (SIP) analyses of these soils revealed that different methanotrophic communities were active in soils under the different vegetations. The C₁₈ PLFAs (signature of type II methanotrophs) predominated under pine and shrublands, and C₁₆ PLFAs (type I methanotrophs) predominated under pastures. Analysis of the methanotrophs by molecular methods revealed further differences in methanotrophic community structure under the different vegetation types. Cloning and sequencing and terminal-restriction fragment length polymorphism analysis of the particulate methane oxygenase gene (pmoA) from different samples confirmed the PLFA-SIP results that methanotrophic bacteria related to type II methanotrophs were dominant in pine forest and shrubland, and type I methanotrophs (related to Methylococcus capsulatus) were dominant in all pasture soils. We report that afforestation and reforestation of pastures caused changes in methane oxidation by altering the community structure of methanotrophic bacteria in these soils.     

Wastewater Irrigation Increases the Abundance of Potentially Harmful Gammaproteobacteria in Soils in Mezquital Valley,Mexico

Wastewater contains large amounts of pharmaceuticals, pathogens, and antimicrobial resistance determinants. Only a little is known about the dissemination of resistance determinants and changes in soil microbial communities affected by wastewater irrigation. Community DNAs from Mezquital Valley soils under irrigation with untreated wastewater for 0 to 100 years were analyzed by quantitative real-time PCR for the presence of sul genes, encoding resistance to sulfonamides. Amplicon sequencing of bacterial 16S rRNA genes from community DNAs from soils irrigated for 0, 8, 10, 85, and 100 years was performed and revealed a 14% increase of the relative abundance of Proteobacteria in rainy season soils and a 26.7% increase in dry season soils for soils irrigated for 100 years with wastewater. In particular, Gammaproteobacteria, including potential pathogens, such as Pseudomonas, Stenotrophomonas, and Acinetobacter spp., were found in wastewater-irrigated fields. 16S rRNA gene sequencing of 96 isolates from soils irrigated with wastewater for 100 years (48 from dry and 48 from rainy season soils) revealed that 46% were affiliated with the Gammaproteobacteria (mainly potentially pathogenic Stenotrophomonas strains) and 50% with the Bacilli, whereas all 96 isolates from rain-fed soils (48 from dry and 48 from rainy season soils) were affiliated with the Bacilli. Up to six types of antibiotic resistance were found in isolates from wastewater-irrigated soils; sulfamethoxazole resistance was the most abundant (33.3% of the isolates), followed by oxacillin resistance (21.9% of the isolates). In summary, we detected an increase of potentially harmful bacteria and a larger incidence of resistance determinants in wastewater-irrigated soils, which might result in health risks for farm workers and consumers of wastewater-irrigated crops.     

Survival of Rhizobium in Acid Soils

A Rhizobium strain nodulating cowpeas did not decline in abundance after it was added to sterile soils at pH 6.9 and 4.4, and the numbers fell slowly in nonsterile soils at pH 5.5 and 4.1. A strain of R. phaseoli grew when added to sterile soils at pH 6.7 and 6.9; it maintained large, stable populations in soils of pH 4.4, 5.5, and 6.0, but the numbers fell markedly and then reached a stable population size in sterile soils at pH 4.3 and 4.4. The abundance of R. phaseoli added to nonsterile soils with pH values of 4.3 to 6.7 decreased similarly with time regardless of soil acidity, and the final numbers were less than in the comparable sterile soils. The minimum pH values for the growth of strains of R. meliloti in liquid media ranged from 5.3 to 5.9. Two R. meliloti strains, which differed in acid tolerance for growth in culture, did not differ in numbers or decline when added to sterile soils at pH 4.8, 5.2, and 6.3. The population size of these two strains was reduced after they were introduced into nonsterile soils at pH 4.8, 5.4, and 6.4, and the number of survivors was related to the soil pH. The R. meliloti strain that was more acid sensitive in culture declined more readily in sterile soil at pH 4.6 than did the less sensitive strain, and only the former strain was eliminated from nonsterile soil at pH 4.8; however, the less sensitive strain also survived better in limed soil. The cell density of the two R. meliloti strains was increased in pH 6.4 soil in the presence of growing alfalfa. The decline and elimination of the tolerant, but not the sensitive, strain was delayed in soil at pH 4.6 by roots of growing alfalfa.     

Effects of DNA Polymer Length on Its Adsorption to Soils

Three different DNA fragments ranging size from 2.69 kbp (1.75 MDa) to 23 kbp (14.95 MDa) were used as tracers to study the adsorption of polydisperse solutions of calf thymus DNA to eight model soils. The adsorption of the three tracers to all soils was described by the Freundlich adsorption model, with adsorption coefficients (K) ranging from 1.1 for acid-washed sand to over 300 for one soil. An inverse relationship between tracer size and K was observed with six of the eight soils, indicating that smaller fragments are sorbed preferentially versus larger fragments in these soils. No significant correlation between K and the organic carbon contents, clay contents, pHs, or cation exchange capacities of the model soils was observed.     

The effect of nutrient application and aeration on oil degradation in soil

Oil degradation was determined in oil-polluted (1 or 2 ml of light Nigerian crude/20 g soil, equivalent to 5 and 10% pollution) soils treated with (NH₄)₂SO₄ and with nutrient elements with and without enhanced aeration. There was no significant difference in oil degradation in soils with and without enhanced aeration, nor in soils treated with and without (NH₄)₂SO₄ and/or nutrients after 4 weeks incubation. After 12 weeks, oil degradation was significantly higher (p = 0·05) in the (NH₄)₂SO₄ and nutrient treated soils in comparison to the untreated soils, and in soils with enhanced aeration in comparison to the undisturbed soil, at the 5% oil pollution level.Warburg respirometer studies showed more oxygen consumption (significant at p = 0·05) in the polluted soils compared with the unpolluted soils. In oil-polluted soils oxygen consumption was depressed significantly (p = 0·05) by the addition of (NH₄)₂SO₄, but was enhanced significantly (p = 0·05) by the addition of (NH₄)₂SO₄ and nutrient elements. The respiratory quotient (RQ) was reduced from 0·81 in unpolluted soils to 0·62 in oil-polluted soils.     

Tracking the origin of the invading Caulerpa (Caulerpales, Chlorophyta) with Geographic Profiling, a criminological technique for a killer alga

The application of the Geographic Profiling technique (with the “Rossmo formula”) proved to be effective in assessing the spreading origin of invading species of Caulerpa in the Mediterranean. Geoprofiling is a technique more frequently used in criminology. We applied this method to an algal invasion for the first time. The method was calibrated with the distribution data of Caulerpa taxifolia, whose spreading in the Mediterranean Sea started from the aquarium of Monaco. This is the first time that Geographic Profiling is calibrated on a data set of sites of presence of a biological invader, of which the spreading origin is known. The application on Caulerpa racemosa var. cylindracea showed that the probable spreading center of the alga should be located in Western Sicily for the Mediterranean and in the southern part of Tenerife for the Canary Islands (Las Galletas, a fishing village). The spreading centers correspond to areas with ports, indicating that the spreading of this alga should be related to (fishing) boats. This result confirmed the opinion of other authors. The parameters used in the Rossmo Formula, obtained through calibration with the known origin of C. taxifolia invasion for identifying the origin of the spread of C. racemosa var. cylindracea may be extended to other algae with similar propagation mode and similar habitat requirements.     

Enhancement of Population Densities of Pseudomonas putida PpG7 in Agricultural Ecosystems by Selective Feeding with the Carbon Source Salicylate

Sodium salicylate (1,000 μg/ml) was delivered through a drip irrigation system to agricultural field soils planted to tomato and infested with Pseudomonas putida PpG7, the host of the salicylate catabolic plasmid NAH7. In nonfumigated soils infested with approximately 10³ CFU of PpG7 per g in the top 30 cm, population densities were increased up to 112-fold within 14 days of the initial application of salicylate compared with the densities in the respective nonamended soils. Mean season-long population densities of PpG7 in the top 30 cm of soil were significantly increased (P < 0.01) from 216 CFU/g in nonamended soils to 1,370 CFU/g in salicylate-amended soils. In the respective rhizosphere soils, mean population densities of PpG7 were significantly increased (P < 0.01) from 92 to 2,066 CFU/cm of root. Soil fumigation interacted (P < 0.01) with salicylate amendment and further increased the mean population densities of PpG7 in nonrhizosphere soil by an additional 5,689 CFU/g of soil. This fumigation effect was not detected in rhizosphere soils. The effect of salicylate in increasing population densities of PpG7 in soil also was affected by inoculum level, field site, and soil depth. Proportionate differences were greater in soils infested with approximately 10³ CFU of PpG7 per g than in comparable soils infested with 10⁵ CFU/g. In low-inoculum soils, increases from salicylate amendments were 26- and 29-fold in rhizosphere and nonrhizosphere soils, respectively, and in high-inoculum soils, the respective increases were 5.6- and 5-fold. No increases of fungi able to utilize salicylate were detected in soils amended with salicylate. However, soil fumigation with metham-sodium significantly reduced (P < 0.01) population densities of fungal salicylate utilizers in rhizosphere and nonrhizosphere soils.