bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of straw management and nitrogen fertilizer on selected soil properties as potential soil quality indicators of an irrigated Dark Brown Chernozemic soil
Authors: Dormaar J. F. , Carefoot J. M.
Published: April 2011

Cereals grown under irrigation in the Canadian prairies produce large amounts of residues. An experiment initiated at the Agriculture and Agri-Food Canada Research Centre, Lethbridge, Alberta, in the fall of 1986, to investigate five straw management treatments (1, chopped straw/fall tillage [straw incorporated]; 2, chopped straw/spring tillage [straw incorporated]; 3, straw baled/fall tillage; 4, straw baled/spring tillage; 5, straw baled/direct seeding) and three fertilizer N rates (0, 100, and 200 kg N ha−1) on crop yields under irrigation, was sampled in April 1995 to examine the effect of straw management and fertilizer additions on selected soil chemical characteristics as potential soil quality indicators. If yield is not used, can we evaluate soil quality from a soil genesis baseline or is it crop growth driven? Differences among straw management and fertility treatments have already supplied information on the effects of these treatments after 8 yr. The treatment in which the straw was baled and the land not tilled had the highest soil bulk density. Total soil organic C and N were highest for the straw baled/no tillage treatment and the 200 kg N ha−1 application. Total C was higher for the fall than spring tillage treatments, while total N was lower for the spring than for the fall tillage treatments when straw was incorporated. Light fraction (mg kg−1 C) was highest for the chopped straw and zero fertilizer additions. For several biologically related characteristics, e.g., mineralizable N, biomass C, biological index N, and hydrolysable N, there were significant interactions between straw management treatments and fertility levels. Monosaccharides at the zero fertility level were generally of microbial origin, while plant-origin monosaccharides were more prevalent as the fertility level increased. It is concluded that the present use does not lead to soil erosion, does not pollute groundwater, and does grow plants; with the help of outside resources, any one straw management treatment can be considered as valid in the anthropocentric sense of soil quality. Since the interpretation of significant effects of treatment on soil properties must be carefully considered depending on the crop selected, the concept of soil quality is thus open to question and debate. Key words: Soil quality, straw management, intrinsic value, tillage, labile organic matter
EPIC estimates of soil water, nitrogen and carbon under semiarid temperate conditions
Authors: Roloff G. , jong R. de , Campbell C. A. , Zentner R. P. , Benson V. M.
Published: April 2011

The Environmental Policy Integrated Climate (EPIC) model is an important support tool for environmental management. Previous tests of the model have determined that it is suitable for long-term yield estimation, but it is less precise in assessing annual yield variability. To determine the reasons for the discrepancies between estimated and measured yields, we tested the ability of EPIC version 5300 to predict soil water and soil nitrogen dynamics, using data from a long-term spring wheat (Triticum aestivum L.) rotation experiment in the semiarid prairie region of Canada. Potential evapotranspiration (PET) estimates varied among methods tested: Priestley-Taylor and Penman-Monteith methods resulted in PET means that were about twice those obtained with the Hargreaves and Baier-Robertson methods. The higher PET means were associated with an excessive estimation of net radiation. We used the Baier-Robertson method to generate the other estimates reported herein. EPIC generally overestimated total soil water, but it still allowed clear differentiation among rotation phases and times of the year, and provided adequate estimates of water during the critical shot-blade stage. Water estimates by soil layer were also generally overpredicted, especially at depths from 0.15 to 0.60 m, but we were able to differentiate among rotation phases and times of the year. Precision of these latter estimates was generally low, accounting at most for 27% of the variability, and varied by soil layer, rotation phase and time of the year. Nitrate-N estimates tended to be lower than measured values, especially at depths below 0.3 m and during vegetative growth phases. However, the estimates also allowed us to distinguish among the rotation phases and times of the year. Total N and organic C were satisfactorily estimated by EPIC. In general, EPIC provided adequate long-term estimates of the environmental quality indicators tested. Key words: Environmental quality, environmental modelling, sustainability, spring wheat, fallow, potential evapotranspiration methods
Impact of tillage and landscape position on nitrogen availability and yield of spring wheat in the Brown soil zone in southwestern Saskatchewan
Authors: Jowkin V. , Schoenau J. J.
Published: April 2011

Nitrogen availability to a spring wheat crop was examined in the cropping season in a side-by-side comparison of no-till (first year) and tillage fallow in an undulating farm field in the Brown soil zone in southwestern Saskatchewan. Thirty different sampling points along a grid in each tillage landscape were randomly selected, representing 10 each of shoulder, footslope and level landscape positions. Nitrogen availability was studied i) by profile inorganic N content ii) by crop N uptake and yield of spring wheat (Triticum aestivum L.) and iii) by 15N tracer technique and in situ burial of anion exchange resin membranes (AEM).Pre-seeding available moisture content of the surface soil samples was significantly higher under no-till compared with tillage fallow. However, no significant differences in pre-seeding profile total inorganic N, crop N uptake and yield were observed between the treatments. At the landform scale, shoulder positions of the respective tillage systems had lower profile inorganic N, crop N uptake and yield compared with other slope positions. Soil N supply power, as determined by 15N tracer and AEM techniques, was not significantly different between the tillage treatments, indicating that N availability is not likely to be greatly affected in initial years by switching to no-till fallow in these soils under normal moisture conditions. Key words: Summerfallow, landscape, nitrogen, wheat
Comparison of porosity in a Chernozemic clay loam soil under long-term conventional tillage and no-till
Authors: Miller J. J. , Kokko E. G. , Kozub G. C.
Published: April 2011

Tillage practice can alter soil structure, porosity and the size distribution of pores. Consequently, this study was conducted to compare the long-term (since 1968) effects of conventional tillage (CT) using a heavy-duty cultivator and no-till (NT) on structure and porosity of a Dark Brown Chernozem (clay loam) soil in southern Alberta. Number and porosity of total, round, intermediate and elongated pores, maximum equivalent circular diameter (MECD), and mean circularity of pore sizes 50–500 µm (P-150), 500–1000 µm (P-500) and >1000 µm (P-1000) diameter were quantified. These parameters were determined for three depths (0–10, 10–20 and 20–30 cm) and two orientations (vertical, horizontal) using UV-dye impregnated soil sections and image analysis. The surface soil (0–10 cm) of CT was dominantly granular-spongy, but for NT it was dominantly crack to massive. Since tillage treatments were not replicated, only general trends on the effect of tillage and its interaction with depth and orientation are given and probability levels are not reported. Tillage treatment had an influence on P-150 and P-500 pores but little or no influence on P-1000 pores. Mean number and porosity of total and intermediate P-500 pores, which are the most important pore size class for seedling root growth in these soils, were higher for CT than NT for the surface soil, but were higher for NT than CT for the subsoil. For example, the total porosity of P-500 pores was 2.21% for CT and 1.95% for NT at the 0- to10-cm depth, 3.80% for NT and 2.27% for CT at the 10- to 20-cm depth, and 3.18% for NT and 2.80% for CT at the 20- to 30-cm depth. These results suggested a higher potential for seedling root growth in the surface soil of CT, but a greater potential for root growth in the subsoil of NT. Key words: structure, porosity, image analysis, tillage
Seasonal comparison of soil temperature and moisture in pits and mounds under vine maple gaps and conifer canopy in a coastal western hemlock forest
Authors: Schmidt Margaret G. , Ogden Aynslie E. , Lertzman Kenneth P.
Published: April 2011

In this study we attempted to determine if vine maple priority gaps show similar trends in temperature and moisture status to those reported in the literature for treefall gaps and whether temperature and moisture status differed between microtopographic positions (pits and mounds). Biweekly measurements of mid-day soil and air temperature, moisture contents at 30-, 50- and 80-cm depths, and depths to the groundwater table were made in pit and mound locations within six vine maple priority gaps paired with six conifer canopy sites. Trends did not follow those found in treefall gaps: vine maple gaps had similar mid-day temperature and moisture status to the surrounding conifer forest. Larger gaps had higher mid-day air temperatures in the summer, higher mid-day soil temperatures in the spring and summer, and greater amounts of throughfall in the spring and summer than smaller gaps. Trends in mid-day soil temperature and moisture status for pit and mound microtopography followed those reported in the literature. Pits were significantly cooler in summer and warmer in winter than mounds and pits were wetter than mounds in all seasons. This study suggests that soil microtopography has an effect on soil climate that overwhelms the influence of vine maple gaps. Key words: Vine maple, canopy gap, soil moisture, soil temperature, microtopography, pits and mounds
Can the plant availability of elemental sulfur be enhanced through its combination with sewage sludge and hydrated lime?
Authors: Sulewski G. D. , Schoenau J. J.
Published: April 2011

Elemental sulfur (S°) was combined with dried anaerobically digested sewage sludge (DDS) and/or hydrated lime (Ca(OH)2) to create a possible alternative to conventional S° fertilizers. These S° blends were studied in both powdered and pelletized form to discern both the role of DDS as a fertilizer binder and as a potential stimulator of heterotrophic S° oxidation. The S° blends were visually examined to obtain general conclusions regarding surface characteristics and potential plant availability. An incubation lasting 12 wk was used to examine the short-term release of sulfate from fine (mean particle diameter [MPD] = 82 µm) and coarse (MPD = 353 µm) S° blends. Sulfate supply potential and the effects of S° pelletization were studied in the growth chamber with canola as the test crop. An apparent link existed between enhanced S° oxidation rate and a modified surface environment produced by the combination of S° + DDS + Ca(OH)2. Soil amendment with S° blends containing DDS + Ca(OH)2 or Ca(OH)2 showed initial oxidation rates superior to S° alone. Growth chamber observations revealed higher canola yield and sulfate recovery with application of S° blends containing DDS + Ca(OH)2 over S° alone. Attempts at pelletizing the S° blends resulted in improved handling characteristics, but lowered product performance due to poor dispersion in soil. Key words: Elemental sulfur, sewage sludge, oxidation, plant availability
Biological Systems Modelling Workshop/ Atelier sur la modélisation des systèmes biologiques
Authors: Pattey Elizabeth , Jong Reinder De
Published: April 2011

not available
Relations entre stabilité de l'agrégation et matière organique totale et soluble à l'eau chaude dans des sols ferrallitiques argileux (Congo, Brésil)
Authors: Kouakoua E. , Larré-Larrouy M.-C. , Barthès B. , Freitas P. L. de , Neves C. , Sala G.-H. , Feller C.
Published: April 2011

Organic matter (OM) generally plays an important role in soil aggregate stability. The objective of this work was to characterize the hot water-extractable OM and its role in the aggregate stability of clayey ferrallitic soils under different land use management. The macroaggregate (>200 µm) stability of these soils was determined before (AS) and after hot-water extraction (ASe). The contents in total organic carbon and in carbon present as carbohydrates, as well as the sugar composition, were determined on the bulk soils and their hot-water extracts.The carbon and macroaggregate contents decreased upon land-clearing and cultivation, but to a lesser extent when some cultural practices were used. Whatever the situation considered, the hot-water extract always presented a higher carbohydrate content than the bulk soil. The high values of ratios r = (galactose + mannose)/(arabinose + xylose) suggested that a large proportion of carbohydrates was of microbial origin. There were significant correlations between AS and the carbon content of bulk soils or hot-water extracts, and between AS and the soil carbohydrate content. On the opposite, whatever the soil sample studied, no significant difference could be found between AS and ASe, showing that hot-water extractable OM had thus no clear aggregating role in these soils. Key words: Organic matter, macroaggregate stability, hot-water extraction, carbohydrates, ferrallitic soils
Field evaluation of anion exchange membranes as a N soil testing method for grasslands
Authors: Ziadi N. , Simard R. R. , Allard G. , Lafond J.
Published: April 2011

The in situ use of anion exchange membranes (AEMs) as a soil-testing procedure may provide a more precise evaluation of N availability to forages than standard methods. The main objective of this study was to evaluate the potential of AEMs to predict soil NO3–N availability for forage production in the western part of the province of Quebec, Canada. In 1995 and 1996, AEMs were buried (0–15 cm) in soils at four sites. The fertilizer treatments consisted of five NH4NO3 rates (0, 60, 120, 180, and 240 kg N ha–1). At all sites, NO3−sorbed on the AEMs (NO3AEMs) increased with increasing N fertilizer rates. The NO3AEMs fluxes were significantly related to water soluble NO3–N (NO3w) concentration in soil (R2 varied from 0.35 to 0.98) in the two growing seasons. Forage N uptake was better related with NO3AEMs fluxes (R2 = 0.88 and 0.92 in spring 1996 and 1995, respectively) than with NO3w concentration (R2 = 0.39 and 0.97 in spring 1996 and 1995, respectively). Based on their simplicity, rapidity, and low cost, AEMs have many practical advantages over water NO3–N extraction for assessing grass forage soil N availability in cool continental climates. Key words: Resin, nitrogen, N uptake, grass forage, N mineralization
Mafic-ultramafic soils affected by silicic colluvium in the Sierra Nevada Mountains (southern Spain)
Authors: Sánchez-Marañón M. , Gámiz E. , Delgado G. , Delgado R.
Published: April 2011

Soil properties, mineral composition, available microelements for plant uptake and ultramicromorphological gravel characteristics in skeletal soils from amphibolite and serpentinite rocks with additions of silicon-rich colluvial materials were studied in the Mediterranean region (Sierra Nevada, southern Spain). The soils (Entic Cryumbrept, Typic Xerochrept, Pachic Cryoboroll and Typic Cryorthent) showed mineralogical discontinuities, exchangeable Ca:Mg ratios greater than 1 and a pH and base saturation profile that decreases in the central and lower parts of the solum. The different soil particle-size fractions had similar mineral compositions (X-ray diffraction [XRD] and infrared [IR] techniques) retaining unstable phases (amphibole, feldspar, serpentine). Inherited or slightly transformed phyllosilicates (serpentine, mica, chlorite, talc and interstratified phases) were shown to be dominant in the clay fraction. The scant pedogenic evolution contrasted with a high free iron content. The concentrations in fine earth of DTPA-Zn, -Cu, -Mn, -Co, -Cr, -Ni and -Fe were not toxic, showed interdependence and were related to the silt, clay and free forms content. The gravel fraction revealed significant amounts of free iron and available microelements (DTPA-extractable), which could be bound to deposits of precipitated secondary forms and to finer pedogenic material present in the fragments. Scanning electron microscope (SEM) observations confirmed these morphological characteristics in serpentinite and amphibolite pebbles. Key words: Mafic-ultramafic soils; mineralogy; DTPA-microelements; rock fragments
Impacts of forage grazing and cultivation on near-surface relative compaction
Authors: Twerdoff D. A. , Chanasyk D. S. , Mapfumo E. , Naeth M. A. , Baron V. S.
Published: April 2011

The study was conducted at the Lacombe Research Station, Alberta, on an Orthic Black Chernozem of loam to silt loam texture to investigate grazing impacts and cultivation on near-surface soil compaction. Four forages, smooth bromegrass (Bromus inermis Leyss 'Carlton'), meadow bromegrass (Bromus riparius Rhem 'Paddock'), a mixture of triticale (X Triticosecale Wittmack 'Pika') and barley (Hordeum vulgare L. AC Lacombe), and triticale were used for the study. Each forage species was subjected to heavy, medium and light intensity grazing. Measurements of bulk density and volumetric moisture content for the 0- to 10-cm depth interval were conducted using a surface moisture-density probe between spring 1994 and fall 1996. Relative compaction was calculated as the actual bulk density expressed as a percentage of the Proctor maximum density. Relative compaction values for all treatments and that for the benchmark were less than 90%, which is considered critical for limiting plant growth. Cultivation reduced bulk density under annual forages by only 3% and lowered it under heavy grazed annual treatments most. Regression analysis conducted on the dependence of bulk density to cumulative cow-days indicated a curvilinear relationship. Bulk density increased more rapidly with increasing cumulative cow-days for annuals compared to perennials. From a management perspective, adopting intensive rotational grazing systems for perennial and annual forages may not cause any serious surface compaction problems for soils in this area. Key words: Annuals, bulk density, cow-days, grazing intensity, perennials, volumetric moisture content
Overwinter soil nitrogen dynamics in seasonally frozen soils
Authors: Ryan M. C. , Kachanoski R. G. , Gillham R. W.
Published: April 2011

An overwinter soil-monitoring study was conducted at two sites in southern Ontario. Soluble soil N accumulation at both sites occured in early winter, peaked when soil water was frozen, and then declined during the period that frozen soil water was present. The amount of soluble soil N accumulated was 48 ± 12 kg N ha−1 at one site, and 21 ± 6 kg N ha−1 at the other. In both cases, the overwinter accumulation approximately doubled the amount of soluble N in the soil. Similar trends were observed in both mineral and organic N, with 60 to 74% of the accumulation occurring in the organic form. No clear correlations between soluble nitrogen dynamics and soil extractable organic carbon or soil microbial biomass carbon dynamics were observed. Denitrification apparently occurred in shallow soil during the thaw period at one site. Since soil nitrate levels decreased before significant thawing occurred, leaching was probably not the primary dissipation mechanism. We hypothesize that the soluble N accumulation was due to death and lysis of soil microorganims during freezing and thawing. The presence of soil ice apparently decreased the lethality of the soil enviroment, allowing N dissipation to occur. Soil N dissipation could be due to gaseous losses, and is likely related to significant N2O fluxes commonly observed during spring thaw. Key words: Nitrogen, overwinter, soil ice
Recipe for 1‐D Lagrangian particle tracking models in space‐varying diffusivity
Authors: Ross Oliver N. , Sharples Jonathan
Published: April 2011

We present a simple recipe to design a physically realistic and robust Lagrangian particle tracking model, paying particular attention to the pitfalls that are associated with the particle tracking if the turbulent mixing is taken as spatially nonuniform. These pitfalls are often neglected or ignored in Lagrangian biophysical particle tracking models and, using simple examples, it is shown how this may lead to physically and hence biologically unrealistic results. Issues associated with the direct particle tracking process are discussed. The choice of a suitable random walk model, in conjunction with an adequate random number generator, is discussed. Two methods are described to correctly implement the reflecting boundary condition in the random walk model, to avoid artificial accumulations at the boundaries. We also examine the more general question of whether the particle diffusivity can be assumed to equal the fluid diffusivity and briefly address the post‐simulation treatment of the data.
Novel techniques for collection of sinking particles in the ocean and determining their settling rates
Authors: Peterson Michael L. , Wakeham Stuart G. , Lee Cindy , Askea Meaghan A. , Miquel Juan Carlos
Published: April 2011

Three new approaches for collecting and processing sinking particles for biogeochemical studies are presented. They include (1) a modification of our existing indented rotating sphere carousel (IRSC) sediment trap design from its conventional time‐series function to one that collects particles based on discrete particle settling‐velocity ranges; (2) development of a large, free‐floating NetTrap based on the design of a closing plankton net capable of collecting large amounts (~1 g) of very fresh sinking particulate material in short time periods (24–36 h) to facilitate microbial decomposition experiments; and (3) an elutriation system to fractionate particles from the NetTrap into settling‐velocity classes using countercurrents of varying speeds. These approaches were recently tested in the Mediterranean Sea and appear to provide new opportunities to characterize fluxes of carbon and other elements of interest and to investigate mechanisms of sinking.
Taxonomic descriptions of three marine colepid ciliates, Nolandia sinica spec. nov., Apocoleps caoi spec. nov. and Tiarina fusa (Claparède & Lachmann, 1858) Bergh, 1881 (Ciliophora, Prorodontida)
Authors: Chen Xiangrui , Gao Shan , Liu Weiwei , Song Weibo , Al-Rasheid Khaled A. S. , Warren Alan
Published: April 2011

The morphology of three marine colepid ciliates,Nolandia sinicaspec. nov.,Apocoleps caoispec. nov. andTiarina fusa(Claparède&Lachmann, 1858) Bergh, 1881, isolated from Chinese coastal waters, was investigated.N. sinicaspec. nov. may be separated from its congeners by the structure of its armour plates, each of which may have up to five reniform windows.A. caoispec. nov. is characterized by its large body with broad anterior end and by having 10–12 long, sharp posterior spines. New data and an improved diagnosis are supplied forTiarina fusa(Claparède&Lachmann, 1858) Bergh, 1881, which has a spindle-shaped body, about 16 ciliary rows and a single adoral organelle. Sequence similarities with other available colepid species were determined.
Streptomyces qinglanensis sp. nov., isolated from mangrove sediment
Authors: Hu Huo , Lin Hai-Peng , Xie Qingyi , Li Lei , Xie Xin-Qiang , Hong Kui
Published: April 2011

A Streptomyces-like strain, 172205T, was obtained from mangrove soil collected at Qinglan Harbour, Wenchang, Hainan, China. The strain was characterized by white aerial mycelium and long spore chains. Comparison of 16S rRNA gene sequences indicated that the strain represents a novel member of the genus Streptomyces, exhibiting highest levels of similarity (<98.29 %) to the type strains of members of the genus Streptomyces. However, DNA–DNA relatedness and phenotypic data readily distinguished strain 172205T from phylogenetically related type strains. The predominant menaquinones were MK-9(H6) and MK-9(H8). The major fatty acids were iso-C15 : 0 (10.31 %), anteiso-C15 : 0 (35.19 %), iso-C16 : 0 (20.24 %) and anteiso-C17 : 0 (10.05 %). The diagnostic phospholipid was phosphatidylethanolamine. The cell wall contained ll-diaminopimelic acid and meso-diaminopimelic acid and whole-cell hydrolysates contained ribose, galactose and glucose. The results of DNA–DNA hybridization, physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain 172205T from phylogenetically related type strains. Therefore, strain 172205T is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces qinglanensis sp. nov. is proposed. The type strain is 172205T ( = CGMCC 4.6825T  = DSM 42035T).
Aquipuribacter hungaricus gen. nov., sp. nov., an actinobacterium isolated from the ultrapure water system of a power plant
Authors: Tóth E. M. , Kéki Zs. , Bohus V. , Borsodi A. K. , Márialigeti K. , Schumann P.
Published: April 2011

A Gram-positive actinobacterium, strain IV-75T, was isolated by using R2A agar from the ultrapure water system of a power plant in Hungary. The strain exhibited a rod–coccus cell cycle, and was strictly aerobic, non-motile, catalase-positive and oxidase-negative. 16S rRNA gene sequence analysis revealed that strain IV-75T belonged to the suborder Micrococcineae and clustered with members of the family Intrasporangiaceae. Its closest phylogenetic neighbour was Arsenicicoccus bolidensis CCUG 47306T (94.3 % 16S rRNA gene sequence similarity). The peptidoglycan of strain IV-75T contained meso-diaminopimelic acid and MK-10(H4) was the major menaquinone. The polar lipid pattern contained phosphatidylglycerol, two unidentified phospholipids, one glycolipid and several other lipid components. The major fatty acids were anteiso-C15 : 0, C18 : 1ω9c and C16 : 0. Based on the moderate levels of 16S rRNA gene sequence similarity to all members of the family Intrasporangiaceae and the unique combination of chemotaxonomic characteristics, strain IV-75T is considered to represent a novel species of a new genus, for which the name Aquipuribacter hungaricus gen. nov., sp. nov. is proposed. The type strain of Aquipuribacter hungaricus is IV-75T ( = DSM 21674T = NCAIM B 02333T).
Immunoglobulin Subclass Profiles of Anti‐idiotypic Antibodies to GAD65Ab Differ Between Type 1 Diabetes Patients and Healthy Individuals
Authors: Oak S. , Radtke J. , Törn C. , Landin‐Olsson M. , Hampe C. S.
Published: April 2011

Previously we reported the presence of anti‐idiotypic antibodies (anti‐Id)‐specific to autoantibodies against GAD65 (GAD65Ab) in healthy individuals while the activity of anti‐Id directed to GAD65Ab in type 1 diabetes (T1D) patients was significantly lower. These anti‐Id recognize the antigen‐binding site of GAD65Ab, thus preventing their binding to GAD65. Here, we characterized the IgG subclass profile of these anti‐Id (GAD65Ab specific) and of the associated GAD65Ab themselves. The IgG subclass response of anti‐Id in healthy individuals (n = 16) was IgG3‐dominated, while in T1D patients (n = 8) IgG1 was the major IgG subclass. The GAD65Ab bound by anti‐Id in both healthy individuals (n = 38) and GAD65Ab‐negative T1D patients (n = 35) showed a predominant rank order of IgG1 > IgG2 > IgG4 > IgG3. However, the frequency of GAD65Ab of the IgG4 subclass was significantly higher in T1D patients (P < 0.05). We conclude that the IgG subclass profile of anti‐Id (GAD65Ab specific) in healthy individuals differs from that in T1D patients. These differences may provide insights into the development of these antibodies.
STARTS – A stable root transformation system for rapid functional analyses of proteins of the monocot model plant barley
Authors: Imani Jafargholi , Li Liang , Schäfer Patrick , Kogel Karl‐Heinz
Published: April 2011

Large data sets are generated from plants by the various ‘omics platforms. Currently, a limiting step in data analysis is the assessment of protein function and its translation into a biological context. The lack of robust high‐throughput transformation systems for monocotyledonous plants, to which the vast majority of crop plants belong, is a major restriction and impedes exploitation of novel traits in agriculture. Here we present a stable root transformation system for barley, termed STARTS, that allows assessment of gene function in root tissues within 6 weeks. The system is based on the finding that a callus, produced on root induction medium from the scutellum of the immature embryo, is able to regenerate roots from single transformed cells by concomitant suppression of shoot development. Using Agrobacterium tumefaciens‐mediated transfer of genes involved in root development and pathogenesis, we show that those calli regenerate large amounts of uniformly transformed roots for in situ functional analysis of newly expressed proteins.
Gene Expression and Immunolocalization of Fibroblast Growth Factor 2 in the Ovary and Its Effect on the In Vitro Culture of Caprine Preantral Ovarian Follicles
Authors: Almeida AP , Saraiva MVA , Alves Filho JG , Silva GM , Gonçalves RFB , Brito IR , Silva AWB , Lima AKF , Cunha RMS , Silva JRV , Figueiredo JR
Published: April 2011

Contents

This study quantified Fibroblast growth factor 2 (FGF‐2) mRNA and localized FGF‐2 protein in different categories of follicles isolated from goat ovaries. In addition, we verified the effects of this factor on the in vitro culture of preantral follicles isolated from goats. For mRNA quantification, we performed real‐time PCR using primordial, primary and secondary follicles, as well as cumulus–oocyte complexes (COCs) and mural granulosa and theca cells of small and large antral follicles. For FGF‐2 protein localization, the ovaries were subjected to conventional immunohistochemical procedures. Preantral follicles were isolated and cultured in vitro for 12 days in either control (basic) or supplemented with FGF‐2 medium. The expression of FGF‐2 mRNA was detected in all categories of follicles and there was no difference in preantral follicles and COCs or granulosa/theca cells from small and large antral follicles. However, in large antral follicles, COCs showed expression levels significantly lower than in granulosa/theca cells (p < 0.05). We observed moderate expression of FGF‐2 protein in preantral follicles but not in granulosa cells of primordial follicles and theca cells of secondary follicles. In both small and large antral follicles, strong, moderate and weak staining was observed in oocytes, granulosa and theca cells, respectively. The addition of FGF‐2 caused a significant increase in the daily follicular growth rate compared to the control group. We conclude that FGF‐2 mRNA is expressed throughout follicular development and that its protein can be found in different patterns in preantral and antral follicles. Furthermore, FGF‐2 increases the follicular growth rate in vitro.
Association of Earthworm-Denitrifier Interactions with Increased Emission of Nitrous Oxide from Soil Mesocosms Amended with Crop Residue
Authors: Nebert Lucas D. , Bloem Jaap , Lubbers Ingrid M. , van Groenigen Jan Willem
Published: April 2011

Earthworm activity is known to increase emissions of nitrous oxide (N
2
O) from arable soils. Earthworm gut, casts, and burrows have exhibited higher denitrification activities than the bulk soil, implicating priming of denitrifying organisms as a possible mechanism for this effect. Furthermore, the earthworm feeding strategy may drive N
2
O emissions, as it determines access to fresh organic matter for denitrification. Here, we determined whether interactions between earthworm feeding strategy and the soil denitrifier community can predict N
2
O emissions from the soil. We set up a 90-day mesocosm experiment in which
15
N-labeled maize (
Zea mays
L.) was either mixed in or applied on top of the soil in the presence or absence of the epigeic earthworm
Lumbricus rubellus
and/or the endogeic earthworm
Aporrectodea caliginosa
. We measured N
2
O fluxes and tested the bulk soil for denitrification enzyme activity and the abundance of 16S rRNA and denitrifier genes
nirS
and
nosZ
through real-time quantitative PCR. Compared to the control,
L. rubellus
increased denitrification enzyme activity and N
2
O emissions on days 21 and 90 (day 21,
P
= 0.034 and
P
= 0.002, respectively; day 90,
P
= 0.001 and
P
= 0.007, respectively), as well as cumulative N
2
O emissions (76%;
P
= 0.014).
A. caliginosa
activity led to a transient increase of N
2
O emissions on days 8 to 18 of the experiment. Abundance of
nosZ
was significantly increased (100%) on day 90 in the treatment mixture containing
L. rubellus
alone. We conclude that
L. rubellus
increased cumulative N
2
O emissions by affecting denitrifier community activity via incorporation of fresh residue into the soil and supplying a steady, labile carbon source.
Genome Sequence of Rhizobium etli CNPAF512, a Nitrogen-Fixing Symbiont Isolated from Bean Root Nodules in Brazil
Authors: Fauvart Maarten , Sánchez-Rodríguez Aminael , Beullens Serge , Marchal Kathleen , Michiels Jan
Published: April 2011

Rhizobium etli
is a Gram-negative soil-dwelling alphaproteobacterium that carries out symbiotic biological nitrogen fixation in close association with legume hosts.
R. etli
strains exhibit high sequence divergence and are geographically structured, with a potentially dramatic influence on the outcome of symbiosis. Here, we present the genome sequence of
R. etli
CNPAF512, a Brazilian isolate from bean nodules. We anticipate that the availability of genome sequences of
R. etli
strains from distinctly different areas will provide valuable new insights into the geographic mosaic of the
R. etli
pangenome and the evolutionary dynamics that shape it.
Characterization of a Zinc-Containing Alcohol Dehydrogenase with Stereoselectivity from the Hyperthermophilic Archaeon Thermococcus guaymasensis
Authors: Ying Xiangxian , Ma Kesen
Published: April 2011

An alcohol dehydrogenase (ADH) from hyperthermophilic archaeon
Thermococcus guaymasensis
was purified to homogeneity and was found to be a homotetramer with a subunit size of 40 ± 1 kDa. The gene encoding the enzyme was cloned and sequenced; this gene had 1,095 bp, corresponding to 365 amino acids, and showed high sequence homology to zinc-containing ADHs and
l
-threonine dehydrogenases with binding motifs of catalytic zinc and NADP
+
. Metal analyses revealed that this NADP
+
-dependent enzyme contained 0.9 ± 0.03 g-atoms of zinc per subunit. It was a primary-secondary ADH and exhibited a substrate preference for secondary alcohols and corresponding ketones. Particularly, the enzyme with unusual stereoselectivity catalyzed an anti-Prelog reduction of racemic (
R
/
S
)-acetoin to (2
R
,3
R
)-2,3-butanediol and
meso
-2,3-butanediol. The optimal pH values for the oxidation and formation of alcohols were 10.5 and 7.5, respectively. Besides being hyperthermostable, the enzyme activity increased as the temperature was elevated up to 95°C. The enzyme was active in the presence of methanol up to 40% (vol/vol) in the assay mixture. The reduction of ketones underwent high efficiency by coupling with excess isopropanol to regenerate NADPH. The kinetic parameters of the enzyme showed that the apparent

K
m

values and catalytic efficiency for NADPH were 40 times lower and 5 times higher than those for NADP
+
, respectively. The physiological roles of the enzyme were proposed to be in the formation of alcohols such as ethanol or acetoin concomitant to the NADPH oxidation.
Identification and Characterization of CdgB, a Diguanylate Cyclase Involved in Developmental Processes in Streptomyces coelicolor
Authors: Tran Ngat T. , Den Hengst Chris D. , Gomez-Escribano Juan Pablo , Buttner Mark J.
Published: April 2011

We describe the identification and functional characterization of
cdgB
(SCO4281), a recently discovered target of BldD, a key regulator of morphological differentiation and antibiotic production in the mycelial bacteria of the genus
Streptomyces
.
cdgB
(
c
yclic
d
imeric
G
MP [c-di-GMP]
B
) encodes a GGDEF-containing protein that has diguanylate cyclase activity
in vitro
. Consistent with this enzymatic activity, heterologous expression of
cdgB
in
Escherichia coli
resulted in increased production of extracellular matrix in colonies and enhanced surface attachment of cells in standing liquid cultures. In
Streptomyces coelicolor
, both overexpression and deletion of
cdgB
inhibited aerial-mycelium formation, and overexpression also inhibited production of the antibiotic actinorhodin, implicating c-di-GMP in the regulation of developmental processes in
Streptomyces
.
Complete Genome Sequence of Strain IMCC9063, Belonging to SAR11 Subgroup 3, Isolated from the Arctic Ocean
Authors: Oh Hyun-Myung , Kang Ilnam , Lee Kiyoung , Jang Yoonra , Lim Seung-Il , Cho Jang-Cheon
Published: April 2011

Strain IMCC9063 is a novel isolate of the SAR11 clade and is distantly related to other cultured representatives in this clade. The strain was isolated off the coast of Svalbard, Norway, by applying high-throughput culturing methods based on dilution to extinction. Here we present the finished genome sequence of strain IMCC9063.
Immunochemical faecal occult blood tests have superior stability and analytical performance characteristics over guaiac-based tests in a controlled in vitro study
Authors: Lee Chun Seng , O'Gorman Paudy , Walsh Paul , Qasim Asghar , McNamara Deirdre , O'Morain Colm A , Boran Gerard P
Published: April 2011

Aims

The aims of this study were (1) to determine the measurement accuracy of a widely used guaiac faecal occult blood test (gFOBT) compared with an immunochemical faecal occult blood test (iFOBT) during in vitro studies, including their analytical stability over time at ambient temperature and at 4°C; and (2) to compare analytical imprecision and other characteristics between two commercially available iFOBT methods.

Methods

Faecal specimens from healthy volunteers negative for occult blood were spiked with red cell lysate to give concentrations of 0 (A), 2.5 (B) and 4.5 (C) mg Hb/g faeces respectively. Samples from each pool were then tested by nine blinded assessors in order to determine the measurement accuracy. Sample stability for the gFOBT at ambient temperature (18°C) was determined by repeating the gFOBT analysis on faecal samples (A, B and C) consecutively for 7 days. Stability for the iFOBT was tested on spiked faecal samples stored at 4°C and also at ambient temperature (18°C). Testing for other analytical performance characteristics including sample carryover and imprecision was performed for both iFOBT methods.

Results

Nine blinded assessors using gFOBT achieved correct readings for eight of nine samples from Pool A, five of nine from Pool B and seven of nine from Pool C. Overall, the sensitivity and specificity of gFOBT were 67% and 89% respectively. No discrepant results were detected with iFOBT. Faecal samples applied to gFOBT cards immediately postcollection gave positive results for the next 7 days only for pool C. In contrast, the results of iFOBT remained stable up to 14 days at 18°C. The within-run imprecision and sample carryover showed robust results with both iFOBT methods.

Conclusions

The superior analytical stability and measurement accuracy demonstrated by the iFOBT in this in vitro study confers advantages over traditional qualitative gFOBTs and supports their suitability for more widespread use in population-based colorectal-cancer screening programmes.
DDE-induced eggshell thinning: an environmental detective story
Authors: Peakall David B.
Published: April 2011

This is a personal account of the investigation of DDE-induced eggshell thinning and the subsequent use of this information in the legal battle over the banning of DDT. The article focuses on the toxicological effects of DDT on the peregrine falcon, Falco peregrinus, although the effects on other species are briefly considered. The peregrine falcon population crashed throughout the Holarctic region in the 1950s and 1960s. Eggshell thinning was discovered in British peregrines in 1967 and was soon found to be a global phenomenon. The relationship between dichlorodiphenyldichloroethylene (DDE) residues and eggshell thinning was established by the beginning of the 1970s. Information on the effect of DDE on the peregrine falcon formed an important part of the evidence that led to the banning of DDT, and since a ban has been implemented in many countries the peregrine populations have improved in most areas.Key words: peregrine falcon, DDE, eggshell thinning.
Environmental fate of mercury from gold mining in the Brazilian Amazon
Authors: Pfeiffer W. C. , Lacerda L. D. , Salomons W. , Malm O.
Published: April 2011

Large quantities of mercury are being released into the waters of the Amazon and its tributaries by gold-mining activities. Large releases are also taking place into the air. In this paper, the fate of mercury released to the environment by gold mining in the Brazilian Amazon is reviewed. Mercury contamination is presently widespread in the Amazon region. A major source of mercury in the local environment is the burning of the gold–mercury amalgam, which releases from 30 to 150 t of mercury yearly into the Amazon atmosphere. Air samples collected close to mining sites showed extremely high mercury concentrations (up to 7.5 μg∙m−3). Inside gold-dealers' shops or in amalgam-burning stations, ambient air concentrations may reach 100 μg∙m−3. A secondary source is the discharge of metallic mercury into rivers during the amalgamation process. Sediment concentrations frequently range from 0.3 to 3.0 μg∙g−1 in contaminated sites. However, values as high as 19.8 μg∙g−1 have been reported in some sites. Waters of many rivers are also contaminated, although reliable data on dissolved mercury concentrations are still lacking. Local carnivorous fishes typically show mercury concentrations higher than 1.0 μg∙g wet wt.−1 in contaminated sites and methyl mercury represents over 90% of the total content. Human groups with fish-based diets frequently show evidence of mercury contamination, with high mercury concentrations in hair (up to 70 μg∙g−1). However, a reliable epidemiological study on the affected population still has to be carried out.Key words: mercury, gold mining, Amazon, sediments, aquatic biota, humans.
Lichens and sulphur dioxide air pollution: field studies
Authors: Seaward M. R. D.
Published: April 2011

The recent spread of air pollution, particularly sulphur dioxide, throughout Europe and elsewhere over the past 200 years is accurately reflected by the decline of lichens. Lichens have proved highly versatile for monitoring not only increasing but also decreasing levels of air pollution in general and, more recently, qualitative differences brought about by changes in energy policies, clean air legislation, and agricultural practices. The use of lichens as biological monitors of sulphur dioxide pollution over the past 150 years is reviewed, and techniques such as zonal mapping, pollution indexes, monitoring scales, and modelling are covered to demonstrate their effectiveness in air quality surveillance, often over wide geographical areas, where physicochemical equipment is often inadequate or indeed nonexistent.Key words: lichens, air pollution, sulphur dioxide, field studies.
Effects of watershed liming on terrestrial ecosystem processes
Authors: Smallidge Peter J. , Brach Anthony R. , Mackun Irene R.
Published: April 2011

Watershed liming has been proposed to mitigate lake acidification and depletion of soil base cations. This paper reviews and synthesizes literature describing the effects of liming on natural terrestrial ecosystems, with a specific emphasis on watershed liming studies. Specifically, we look at the purpose of liming, types of lime, physiological role of calcium, lime effects on soil and belowground processes, and plant response to liming with special attention to growth and tissue chemistry, roots, and plant–plant interactions. Liming increases soil pH and either increases or decreases soil nutrient availability. Liming affects litter decomposition, mineral soil processes, root growth, plant nutrient uptake, and plant productivity. Interspecific plant interactions can be affected after liming. Specific soil and biotic responses depend upon the type and amount of lime applied, the period of observation, soil characteristics, and species composition.Key words: watershed liming, CaCO3, calcite, dolomite, calcium, ecosystem response to liming, wetland liming, forest liming, nutrient availability, soil acidity.
Environmental influences on fish and shellfish production in the Northwest Atlantic
Authors: Mann K.H. , Drinkwater K.F.
Published: April 2011

Evidence is reviewed, linking physical oceanographic processes in the marine environment to changes in fish and shellfish stocks in the Northwest Atlantic. A case history study of the cod (Gadus morhua) stock of the northern Grand Banks and Labrador Shelf indicates a long slow amelioration of the environment between about 1945 and 1965, followed by a deterioration in the period 1965–1992. The most important environmental factors for the cod stocks appear to have been salinity and temperature. The trends can be traced back to climatic factors involving the Icelandic Low and the Azores–Bermuda High. When the atmospheric pressure difference in winter tended to be high, there was a progressive increase in the area of sea ice off Labrador and in the volume of cold water at depth. These factors have been shown to affect temperature and salinity conditions on the Grand Banks in spring and summer and are associated with poor growth and recruitment in the cod stocks. A similar case study of lobster (Homarus americanus) stocks indicates that temperature and river discharge are important environmental correlates, but neither can be shown to fully account for the recent trends in the stocks. Evidence is reviewed to show that physical environmental processes also influence recruitment and distribution of stocks of haddock, capelin, and squid. Some of the problems with correlational analysis are also discussed. It is recognized that factors other than the environment are influencing the stocks. Fishing mortality (detailed consideration of which is not included in this review) has clearly been important. Interactions between environmental factors and fishing mortality are probably of major importance.Key words: ocean environment, fish production, recruitment, northern cod, American lobster.
The arctic tree line as a record of past and recent climatic changes
Authors: Payette Serge , Lavoie Claude
Published: April 2011

Past and recent changes in the position of the arctic tree line and spatial structure of nearby forests are reviewed. The advancing tree line in the arctic tundra in the first half of the Holocene was promoted by sexual regeneration because of warmer climate. The northernmost tree-line positions were reached in early Holocene in western North America and northern Eurasia, and during or after mid-Holocene in central and eastern North America. The position of the arctic tree line remained rather stable across the northern hemisphere from 3500 years BP to the present. General cooling during the late Holocene did not induce significant retreat of the tree line at sites not affected by catastrophic disturbances (fire) because trees and forests were able to survive through vegetative regeneration. Minor displacements deduced from dendroecological data were recorded during the last 500 years, whereas more important structural changes occurred in the nearby northernmost forests and tree groves through the shifting dominance of growth forms in preestablished tree and forest populations. The spatiotemporal pattern of tree-line and forest changes along the arctic border suggests that both equilibrium and nonequilibrium conditions prevailed during the Holocene.Key words: tree line, Arctic, climate change, paleoecology, Holocene.