bluuebunny/crossref_metadata_2025 huggingface dataset:
Évolution des stocks de carbone organique dans le solaprès coupe dans la sapinière à bouleau jaune de l'est du Québec
Authors: St-Laurent Sylvain , Ouimet Rock , Tremblay Sylvie , Archambault Louis
Published: April 2011

Following the Rio and Kyoto protocols, forest sequestration of organic C (Corg) appears to be among the measures to reduce atmospheric C. In this context, we assessed the evolution of soils' reserves of Corg after complete whole-tree forest harvesting in the balsam fir–yellow birch forest of eastern Quebec. The experimental design consisted of eight plots in mature stands, and 10 plots in 7-, 12-, and 22-yr-old clearcuts in the "Seigneurie du Lac Métis", located 80 km south-east of Rimouski, Quebec, Canada. The soil type was an Orthic Humo-ferric Podzol. Major Corg losses occured in the forest floor of the 7-, 12- and 22-yr-old harvested plots compared with mature stands. The FH horizon of harvested plots showed a loss of 44% (−30.5 t ha−1) in dry weight and 13.5% (−62.1 g kg–1) in Corg content between 7 and 22-yr-old harvested plots. More than half the Corg content of the forest floor was lost in that time (−52% or −16.6 t ha−1). The Corg stock of the L horizon were lowered only for the 7-yr-old treatment (2.5 t ha−1) compared with mature stands (4.9 t ha−1). No significant differences in the Corg stocked in the first 30 m of the mineral soil were found between treatments. It appears that the forest floor of balsam fir–yellow birch stands has become a source of Corg for at least 22 yr after forest harvesting. Key words: Forest harvesting, soil, organic carbon, forest floor
Effects of skidding on forest soil infiltration in west-central Alberta
Authors: Startsev A. D. , McNabb D. H.
Published: April 2011

Soil compaction during forest harvesting generally reduces macropore space, which reduces infiltration and increases the potential for surface erosion and waterlogging. Hydrological effects of 3, 7 and 12 skidding cycles and their persistence were evaluated for 3 yr at 14 sites, which represented a range of soil texture and compaction conditions in the foothills and boreal forests of Alberta. Saturated hydraulic conductivity (HC) was determined using a constant head method on soil cores collected from 5- and 10-cm depths; unconfined infiltration rate of the surface soil (IR) was measured in situ with tension infiltrometers at near saturation. A significant (P < 0.05) increase in bulk density during skidding caused a significant reduction in both HC and IR after the first three cycles at eight sites where soil water potential at the time of skidding was higher than −15 kPa; the decrease at the other sites was not significant. Additional traffic, up to 12 cycles, did not cause a further significant decrease in HC or IR. The infiltration rate of soil compacted by three skidding cycles showed a recovery trend. However, in more intensively trafficked soils, compaction effects on infiltration remained significant for at least 3 yr, which was possibly attributed to heavy snowpacks preventing soil freezing at lower depths. Key words: Saturated hydraulic conductivity, unconfined infiltration rate, tension infiltrometers, skidders, boreal forest, Alberta
Pasture type and fertilization effects on soil chemical properties and nutrient redistribution
Authors: Chen W. , McCaughey W P , Grant C A , Bailey L D
Published: April 2011

Soil samples were collected from beef pastures varying in species composition and fertilizer inputs after being grazed by cow-calf pairs for 4 yr (1995-1998) near Brandon, Manitoba. The objective of this experiment is to examine the impact of 4 yr of continuous rotational grazing on soil chemical properties and nutrient redistribution in mixed alfalfa-grass and pure-grass pastures with or without fertilization. Pastures were established on an Orthic Black Chernozemic, fine sandy-loam soil. Compared with N-fertilized pure-grass pastures, alfalfa-grass pastures had greater seasonal soil mineral-N supply, and tended to have higher total soil C, N and organic C. In grazed systems in this environment, the use of alfalfa as the primary N source may be more profitable and sustainable than using fertilizer N. However, considering the seasonal changes in soil nitrification rate observed in alfalfa-grass pastures, caution needs to be taken when stands with high legume content are used to maximize animal performance, because this may increase the risk of N losses into the environment. Fertilization over a 5-yr period (1994-1998) tended to lower surface soil pH. Application of P significantly increased soil “extractable” P levels in the top 15-cm soil layer. However, K fertilization only increased surface soil “extractable” K slightly compared with unfertilized pastures. There was also no effect of S application on soil “extractable” S. Zone effects on soil mineral N and soil “extractable” P, K and S were limited to the surface (0–7.5 cm). For mineral N, the zone effect seemed to be more pronounced in first rotation than in second rotation. The magnitude of K redistribution was greater than for S and P due to higher K intake and excretion. Use of rotational stocking with short grazing periods appears to have resulted in a relatively even redistribution of nutrients derived from animal excreta. Key words: Grazing, beef pasture, nitrogen dynamics, sustainability
Cover crops and nitrogen fertilization effects on soil carbon and nitrogen and tomato yield
Authors: Sainju U. M. , Singh B. P. , Whitehead W. F.
Published: April 2011

Cover crops can influence soil properties and crop yield. We examined the influence of legume [hairy vetch (Vicia villosa Roth) and crimson clover (Trifolium incarnatum L.)] and nonlegume [rye (Secale cereale L.)] cover crops and N fertilization (0, 90, and 180 kg N ha−1) on the short- and long-term effects on soil C and N and tomato yield and N uptake. We measured organic C and N (long-term effects), potential C and N mineralization (PCM and PNM) and inorganic N (short-term effects) periodically on a Greenville fine sandy loam (fine-loamy, kaolinitic, thermic, Rhodic Kandiudults) planted with tomato (Lycopersicum esculentum Mill) from April to August in 1996 and 1997 in Georgia USA. Soil C and N concentrations increased early in the growing season with cover crop residue incorporation, but decreased as the residue decomposed. Rye increased organic N and maintained greater levels of organic C and PCM after 3 yr than other treatments. In contrast, hairy vetch and crimson clover increased PNM and inorganic N soon after residue incorporation into the soil and produced tomato yield and N uptake similar to that produced by 90 and 180 kg N ha–1. Nitrogen fertilization increased PNM and inorganic N after split application and tomato yield and N uptake but decreased organic C and N and PCM compared with rye. Compared with 0 kg N ha–1, nonlegume cover crops, such as rye can increase organic C and N and PCM but legume cover crops, such as hairy vetch and crimson clover, can enrich soil N and produce tomato yield and N uptake similar to that produced by 90 and 180 kg N ha−1. Key words: Cover crops, nitrogen fertilization, soil carbon, soil nitrogen, tomato yield
Diffusive phosphate transport in Al-rich acidic porous cation exchange system
Authors: Ro H. M. , Cho C. M.
Published: April 2011

One-dimensional diffusive phosphate transport in a porous cation-exchange resin model system was investigated to examine the effect of exchangeable Al on the movement of phosphate. This study presumes that Al interacts with phosphate and H+ is produced as a result of deprotonation of H2PO4−. The production of H+ due to interactions between positively charged Al ions and phosphate ions was confirmed by measuring the pH change during the titration of phosphate by aluminum or aluminum by phosphate ions. A set of cylindrical wax columns packed with: (A) a mixture of sand and solid Al2O3, (B) a mixture of sand and Al3+-saturated cation-exchange resin, (C) a mixture of sand, solid Al2O3, and Al3+-saturated cation-exchange resin, and (D) sand as a control was used. A 0.2-g sample of 32P-KH2PO4 was applied on the surface of the mixture in each column simulating one-dimensional diffusion from an instantaneous planar source into a semi-finite system. Retardation of phosphate transport by exchangeable Al3+ was characterized by lowering of pH. Phosphate transport was not retarded in the presence of solid Al2O3 alone. Phosphate movement was further retarded in the presence of exchangeable Al3+ with solid Al2O3. Under this situation, H+ ion produced from precipitation reactions dissolved solid Al2O3, giving rise to more Al3+ in solution. Aluminum ion in the solution phase moved towards the site where phosphate was precipitated. From a mass balance of P, a slight amount of P was not recovered in the system whose pH was kept around 2.0 or below, indicating a probable formation of K-taranakite. Either K-taranakite or K2Al5H7(PO4)8−14H2O was identified as a final precipitation product from a series of titration experiments. However, at least two unidentified morphologically different amorphous aluminum phosphates were observed. Key words: Aluminum, cation-exchange, phosphate, precipitation, retardation, transport
Spectrophotometric pH measurement in the ocean: Requirements, design, and testing of an autonomous charge‐coupled device detector system
Authors: Friis Karsten , Körtzinger Arne , Wallace Douglas W.R.
Published: April 2011

A newly designed system for high quality discrete spectrophotometric measurements of pHT using a low‐cost charge‐coupled device (CCD) detector is described. Considerations and requirements for the choice of spectrophotometers with a CCD detector instead of scanning spectrophotometers with photomultiplier detector are elucidated. The presented system is evaluated in the laboratory for system accuracy and short‐term precision and at sea for long‐term precision and at‐sea capability. Derived system characteristics are a (1s) short‐term precision of ±0.0012 pH units and a (1s) long‐term precision at sea of ±0.0032 pH units based on Certified Reference Materials (CRM). Such long‐term precision is equivalent to a deviation of ±1.1 to 2.2 µmol kg−1 in total dissolved inorganic carbon (TCO2) and ±1.4 to 2.1 µmol kg−1 in total alkalinity (TA), depending on temperature and the TCO2/TA ratio. Overdetermination of the CO2 system (TCO2, TA, pHT) from surface‐to‐deep water profiles support the accuracy and precision assessment in comparison to earlier data. With careful design and testing, low‐cost CCD spectrophotometers can be used for high accuracy pH measurements.
Simultaneous determination of iron reduction and uptake by phytoplankton
Authors: Shaked Yeala , Kustka Adam B. , Morel François M.M. , Erel Yigal
Published: April 2011

We have developed a new method to assess simultaneously the rates of biological reduction of Fe(III)‐ligand complexes at nanomolar concentrations and iron uptake in marine phytoplankton. Other methods for measuring iron reduction require micromolar iron concentrations, which can saturate iron uptake in these organisms. In the present study, high sensitivity was obtained by combining radiometric techniques, ligand competition, and selective retention on solid phase extraction columns (C18 Sep‐Pak©). Following the addition of the Fe(II) specific ligand ferrozine (FZ) to seawater spiked with nanomolar concentrations of radiolabeled iron, the rate of iron uptake is determined by filtering aliquots of cultures, and the rate of Fe(II) binding to FZ by passing the filtrate through a column, which retains the Fe(II)FZ3 complex. The method was calibrated using 55Fe(II) standards in NaCl solution, yielding high recovery efficiency and linear behavior across the entire range tested from 3 × 10−11 M to 2 × 10−6 M Fe(II). Special attention was given to possible artifacts caused by reduction of Fe(III) in the presence of FZ and Fe(III) adsorption onto the column, which are critical when measuring picomolar concentrations of Fe(II). The method was successfully applied to Thalassiosira weissflogii cultures and to natural phytoplankton populations in the Bering Sea using ethylenediaminetetraacetic acid as a model ligand.
Methods for measuring benthic nutrient flux on the California Margin: Comparing shipboard core incubations to in situ lander results
Authors: Hammond Douglas E. , Cummins Kathleen M. , McManus James , Berelson William M. , Smith Gerry , Spagnoli Federico
Published: April 2011

The objective of this study was to compare two techniques for estimating benthic fluxes of nutrients (nitrate, phosphate, and silicic acid) and Ge/Si flux ratios. In situ flux chambers were deployed, and cores were collected and incubated at 9 sites along the California margin in July 2001. Both techniques were successful at 8 sites, at depths from 100 to 3300 m. Flux chambers were deployed for 1 to 2 d, and cores were incubated for slightly longer on board the ship in a cold room. In some cases, core incubation flux temperature varied by up to 5°C from in situ temperature, and core incubation results were adjusted for this factor based on the effects of temperature on diffusivities and the adsorption of silicic acid. Sites studied had a range in nutrient fluxes of more than an order of magnitude, based on in situ chambers. The temperature‐adjusted core incubation fluxes showed a similar, but slightly smaller range. Both methods had similar precision based on replicates, with uncertainties for high flux stations that were 5% to 20% of the mean. Only phosphate showed significant (95% confidence level) spatial variability in replicate cores; the larger in situ flux chambers had less spatial variability. The two techniques did show some systematic differences that are attributed to several artifacts created by core recovery. Silicic acid fluxes from cores were significantly lower than in situ fluxes at 2 sites; overall averages were about 80% of those for in situ chambers. The differences are attributed to reduced macrofaunal irrigation in incubated cores. Nitrate uptake in core incubations at 5 of 8 stations was significantly lower than in situ uptake; shipboard rates for all sites averaged about 66% of in situ chamber rates. This difference is attributed primarily to decreased denitrification rates in recovered cores in response to altered temperature and pressure. Phosphate fluxes from cores were significantly lower at only one site; overall, results for the two techniques were indistinguishable. Only one site had a significantly different Ge/Si flux ratio.
A semi‐automated digital microphotographic approach to measure meiofaunal biomass
Authors: Baguley Jeffrey G. , Hyde Larry J. , Montagna Paul A.
Published: April 2011

Meiofauna studies often investigate community structure and function where biomass estimates and taxonomic analysis are required. Nondestructive methods of biomass estimation are necessary to preserve specimens for subsequent taxonomic analysis. A semi‐automated protocol to estimate meiofaunal biomass was developed to meet this need. The method improves upon previous indirect biomass techniques by using digital microphotography and analytical graphics software to obtain better estimates of biovolume. The technique is not fully automated because the digital images require some manipulation. Dry mass and carbon mass were estimated for two dominant components of marine benthic meiofauna (Nematoda and Harpacticoida) as the product of conversion factors and body volumes. The technique was validated by comparing indirect dry and carbon mass estimates to direct measurements using an analytical balance and carbon‐hydrogen‐nitrogen (CHN) elemental analyzer. No significant difference was found between the semi‐automated method and direct measurements for harpacticoid dry or carbon mass (P = 0.68 and P = 0.74, respectively), or nematode dry mass (P = 0.28) or carbon content (P = 0.17). The semi‐automated indirect method was used to estimate the biomass of meiofauna (13,279 harpacticoids and 12,288 nematodes) collected from the deep‐sea Gulf of Mexico. Estimated average wet mass was compared to direct analytical balance measurements from an earlier, independent study in the same area. Wet mass estimates generated by the indirect method (2.67 ± 0.86 µg/harpacticoid and 0.85 ± 4.78 µg/nematode) were similar to direct measurements in the earlier study (2.80 µg/harpacticoid and 0.85 µg/nematode). The semi‐automated indirect method is about three times faster than traditional microscope methods to measure body volume, estimates biomass comparably to direct methods, and conserves samples and images of samples for other analyses.
Real‐time physical data acquisition through a remote sensing platform on a polar lake
Authors: Palethorpe Ben , Hayes‐Gill Barrie , Crowe John , Sumner Mark , Crout Neil , Foster Malcom , Reid Tim , Benford Steve , Greenhalgh Chris , Laybourn‐Parry Johanna
Published: April 2011

We describe the design and installation of environmental monitoring equipment on a large freshwater Antarctic lake (Crooked Lake, 68°37′S, 78°23′E). The system recorded ice thickness and photosynthetically active radiation (PAR), ultraviolet (UVB) radiation, and temperature at a range of depths in the water column. The data were accessed remotely at Davis Station (15 km distant) by telemetry. The remote sensing platform produced continuous quasi real‐time data, enabling the development of accurate detailed models, e.g., ice heat budget models during seasonal melt out. The prototype system has the capacity for the addition of further instrumentation, for example, fluorimeters. Here we present an illustrative preliminary data set derived during the summer immediately prior to ice‐cover break up and after winter redeployment of the platform.
A novel method for the measurement of dissolved deoxyribonucleic acid in seawater
Authors: Brum Jennifer R. , Steward Grieg F. , Karl David M.
Published: April 2011

A novel method was developed for the quantification of dissolved deoxyribonucleic acid (D‐DNA) in seawater. This method includes addition of tetrasodium ethylenediamine tetraacetic acid (tetrasodium EDTA) to 0.22 µmfiltered seawater, concentration of > 10 kDa material in the filtrate with a Centricon centrifugal concentration unit, and quantification of the concentrated D‐DNA with the fluorescent double‐stranded DNA stain SYBR Green I. This method requires less than 15 mL of seawater per sample even in oligotrophic environments, and samples can be analyzed in approximately 3 h. The recovery of D‐DNA with this method is 75% to 85% and can be determined for each sample by measuring recovery of 35S‐labeled DNA added at trace amounts. This method can be used to quantify D‐DNA concentrations as low as 0.01 ng mL−1 with high precision (standard deviation < 5% of the mean). Deoxyribonuclease (DNase) treatment of samples and virus enumeration can be used in conjunction with this method to determine the three major components of D‐DNA: free or enzymatically hydrolyzable DNA (ehD‐DNA), DNA within viruses, and uncharacterized bound DNA.
The Bunsen gas solubility coefficient of ethylene as a function of temperature and salinity and its importance for nitrogen fixation assays
Authors: Breitbarth Eike , Mills Matthew M. , Friedrichs Gernot , LaRoche Julie
Published: April 2011

The acetylene reduction assay is a common method for assessing nitrogen fixation in a variety of marine and freshwater systems. The method measures ethylene, the product of the conversion of the gas acetylene to its reduced form by nitrogenase. Knowledge of the solubility of ethylene in aqueous solution is crucial to the calculation of nitrogen fixation rates and depends on the temperature and salinity of the assay conditions. Despite the increasing interest in marine nitrogen fixation, no gas solubility (Bunsen) coefficients for ethylene in seawater are published to date. Here, we provide a set of equations and present semiempirically derived Bunsen coefficients for ethylene in water (ranging from 0.069 to 0.226) for a range of temperatures and salinities that are relevant for aquatic nitrogen fixation. We apply these data to nitrogen fixation scenarios at different temperatures and salinities and stress the importance of using accurate Bunsen coefficients in nitrogen fixation assays.
A neuro‐fuzzy modeling tool to estimate fluvial nutrient loads in watersheds under time‐varying human impact
Authors: Marcé Rafael , Comerma Marta , García Juan Carlos , Armengol Joan
Published: April 2011

Fluvial nutrient loads are usually calculated through a bilogarithmic regression relating flow and river nutrient concentration. This relationship, however, can be highly nonlinear, due to changes in watershed land uses over time. Also, retransformation of data can result in important biases, and available databases usually do not provide the statistical properties needed to apply parametric statistics or time‐series analysis methods. The validity and advantages over customary methods of an Adaptive Neuro‐Fuzzy Inference System (ANFIS) for estimating fluvial nutrient loads in watersheds under time‐varying human impact was tested. Fluvial nutrient loads time‐series were modeled in two watersheds of different size and human impact history. ANFIS and methods based on rating curves and ratio estimators were applied to compare results. The ANFIS approximation gave unbiased estimates of loads and showed advantages over the other methods: It allowed the implementation of a homogeneous, model‐free methodology throughout the data series, avoiding the presence of artifacts in the final load histories; it fitted the observed concentration time‐series better than the other procedures; it worked in real space without the need to logarithmically transform and retransform data; and it gave annual dispersion values, which could be interpreted as annual uncertainties. In addition, the parameters fitted during the ANFIS modeling could be ecologically interpreted, and were a valuable tool to describe features of modeled data and to understand historical changes in human impact on watersheds. MATLAB codes and instructions to implement the new method are provided.
A new sampling device for microaggregates in turbid aquatic systems
Authors: Lunau Mirko , Sommer Andreas , Lemke Andreas , Grossart Hans‐Peter , Simon Meinhard
Published: April 2011

Microaggregates (5 to 500 µm) are the main component of suspended particulate matter in shallow and turbid aquatic environments. Whereas their abundance and size structure have been studied by various optical systems, their composition, aggregation and disaggregation processes, and microbial colonization have been studied only little. This is largely due to inadequate sampling devices for microaggregates. Therefore, we established a new device, allowing the careful collection and documentation of aggregate size and abundance by laser illumination and a regular digital camera. The instrument simultaneously serves as a settling chamber to separate and subsample microaggregate fractions, differing in their settling velocities. Thus, it provides material for studying the biological and chemical composition and microbial colonization of microaggregates with a minimum of manipulation. First results from its application during a semitidal cycle in the German Wadden Sea demonstrate that it yields reliable results of the abundance and size structure of aggregates, reflecting the tidal changes in the hydrodynamic conditions. Total aggregate abundance covaried with dry weight of suspended particulate matter and turbidity. The biological and chemical analysis of aggregate fractions separated during 45 min of settling, showed that the various fractions exhibited distinct differences with respect to aggregate size, dry weight, particulate organic carbon, the carbon per nitrogen ratio (by weight), number of bacteria and bacterial production rates per aggregate. Hence, the application of this sampling device will lead to better insight into the dynamics and qualitative changes of microaggregates in turbid aquatic systems and deepen our understanding of their overall significance in these ecosystems.
High‐frequency measurement of seawater chemistry: Flow‐injection analysis of macronutrients
Authors: Hales Burke , van Geen Alexander , Takahashi Taro
Published: April 2011

We adapted a commercially available flow‐injection autoanalyzer (Lachat Quik‐Chem 8000) to measure seawater nitrate concentrations at a rate of nearly 0.1 Hz and phosphate and silicate concentrations at a rate half that. Several minor improvements, including reduced sample‐loop size, high sample flushing rate, modified carrier chemistry, and use of peak height rather than peak area as a proxy for nutrient concentration aided in the increase in sampling rate. The most significant improvement, however, was the construction of a copperized cadmium NO3− reduction column that had a high surface area to volume ratio and a stable packing geometry. Preliminary results from a cruise in the Ross Sea in austral spring of 1997 are shown. Precision of all three analyses is better than 1%. Comparison of the nutrient concentrations determined by the rapid analysis method described here with traditional discrete analyses shows that nitrate and silicate determined by the two approaches are within a few percent of each other, but that the phosphate concentrations determined by the rapid analysis are as much as 10% lower than those determined by the discrete analyses.
An estuarine observatory for real‐time telemetry of migrant macrofauna: Design, performance, and constraints
Authors: Grothues Thomas M. , Able Kenneth W. , McDonnell Janice , Sisak Mitchell M.
Published: April 2011

In 2002, we began tagging macrofauna and established an array of hydrophones in the Mullica River and Great Bay estuary in southern New Jersey, USA, as part of an observatory for the study of migration. The hydrophone array differs from other model telemetry programs in several aspects. The wireless radio‐linked design provides the capability to couple observation in real time with reactive sampling schemes (including mobile tracking), provides for public interaction via frequent updates to a Worldwide Web‐based distance learning program, and saves ship time. However, the wireless design is more amenable to a turnstile‐like acoustic gate than to positioning, and strategic positioning of hydrophones at bottlenecks is favored over continuous contact of transmitters within the large study area. The hydrophone array is supplemented by infrastructure from two existing marine observatory programs focused on physical processes. These are the Long‐term Ecosystem Observatory (LEO‐15) outside the estuarine inlet and the System‐Wide Monitoring Program of the Jacques Cousteau National Estuarine Research Reserve (JCNERR) within the river and estuary. This article outlines considerations in the design and implementation of the array from infrastructure, predeployment survey, and biological considerations through hydrophone placement, maintenance, calibration, and data collection. Further, it presents a comprehensive description of the observatory and study area for reference in works on the biology of those organisms under study. The hydrophone array serves as a unit intended for stepwise extension into other estuaries to assist in our understanding of habitat use and of those species that use estuarine habitat during coastal migration.
Rhizon sampling of porewaters near the sediment‐water interface of aquatic systems
Authors: Seeberg‐Elverfeldt Jens , Schlüter Michael , Feseker Tomas , Kölling Martin
Published: April 2011

Rhizon samplers were originally designed as micro‐tensiometers for soil science to sample seepage water in the unsaturated zone. This study shows applications of Rhizons for porewater sampling from sediments in aquatic systems and presents a newly developed Rhizon in situ sampler (RISS). With the inexpensive Rhizon sampling technique, porewater profiles can be sampled with minimum disturbance of both the sediment structure and possible flow fields. Field experiments, tracer studies, and numerical modeling were combined to assess the suitability of Rhizons for porewater sampling. It is shown that the low effort and simple application makes Rhizons a powerful tool for porewater sampling and an alternative to classical methods. Our investigations show that Rhizons are well suited for sampling porewater on board a ship, in a laboratory, and also for in situ sampling. The results revealed that horizontally aligned Rhizons can sample porewater with a vertical resolution of 1 cm. Combined with an in situ benthic chamber system, the RISS allows studies of benthic fluxes and porewater profiles at the same location on the seafloor with negligible effect on the incubated sediment water interface. Results derived by porewater sampling of sediment cores from the Southern Ocean (Atlantic sector) and by in situ sampling of tidal flat sediments of the Wadden Sea (Sahlenburg/Cuxhaven, Germany) are presented.
Extracting growth rates from the nonlaminated coralline sponge Astrosclera willeyana using bomb radiocarbon
Authors: Fallon Stewart J. , Guilderson Thomas P.
Published: April 2011

The isotopic and chemical composition of the skeletons of hermatypic reef building corals have been used for many years to generate proxy time series records of surface oceanic conditions (water temperature and salinity). These types of records have recently been constructed using coralline sponges. Because they are found in a greater range of depths, coralline sponges have the potential to fill in gaps in our understanding of subsurface oceanographic variability. Using coralline sponges together with surface corals, we can obtain a threedimensional (3D) picture of oceanographic/climate variability. However, coralline sponges have one disadvantage compared to hermatypic reef building coral proxies in that most do not have annual density bands and need to be radiometrically dated for age determination. We have measured radiocarbon in 1 mm increments from Astrosclera willeyana sponges collected off the Central and Northern Great Barrier Reef (GBR) and from Truk in the Caroline Islands and compared these radiocarbon profiles to independently dated coral radiocarbon records to examine growth rate variability. Growth rates of the GBR sponges averaged 1.2 ± 0.3 and 1.0 ± 0.3 mm y−1 at north and central sites respectively, but the growth rate can vary by a factor of two over the life span of the sponge. The growth rate of the Truk sponge averaged 1.2 ± 0.1 mm y−1. These growth rates are faster than those measured for other Astrosclera willeyana sponges (0.2–0.7 mm y−1) (Moore et al. 2000; Wörheide 1998).
Corallibacter vietnamensis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae
Authors: Kim Seung Bum , Nedashkovskaya Olga I. , Zhukova Natalia V. , Kuchlevskiy Andrey D. , Mikhailov Valery V.
Published: April 2011

The taxonomic position of two strains of a novel heterotrophic, strictly aerobic, Gram-negative, gliding, dark-orange-pigmented bacterium, designated KMM 6217T and KMM 6332, was determined. The strains grew at 10–40 °C and with 0.5–8.0 % NaCl. They were catalase- and oxidase-positive, produced flexirubin-type pigments and hydrolysed aesculin, gelatin, starch, Tween 80 and DNA. The predominant fatty acids were iso-C15 : 1, iso-C15 : 0, C15 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The polar lipid profile comprised phosphatidylethanolamine as the major component, three unknown aminolipids and one unknown lipid. The DNA G+C content was 34.7–34.8 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that the novel isolates could be placed in the family Flavobacteriaceae. The nearest neighbours of strains KMM 6217T and KMM 6332 were members of the genera Bizionia, Formosa, Lacinutrix, Meridianimaribacter, Mesoflavibacter and Winogradskyella, with sequence similarities to the type strains of species of these genera of 92.8–95.2, 93.7–94.5, 94.1–94.7, 94.9, 94.6 and 93.5–94.4 %, respectively. Based on phenotypic, genotypic and phylogenetic data, strains KMM 6217T and KMM 6332 should be classified as representatives of a novel species in a new genus in the family Flavobacteriaceae of the phylum ‘Bacteroidetes’, for which the name Corallibacter vietnamensis gen. nov., sp. nov. is proposed; the type strain is KMM 6217T ( = JCM 17525T = KCTC 23026T).
Characterization of Defluviitalea saccharophila gen. nov., sp. nov., a thermophilic bacterium isolated from an upflow anaerobic filter treating abattoir wastewaters, and proposal of Defluviitaleaceae fam. nov.
Authors: Jabari Linda , Gannoun Hana , Cayol Jean-Luc , Hamdi Moktar , Fauque Guy , Ollivier Bernard , Fardeau Marie-Laure
Published: April 2011

A novel thermophilic, anaerobic, Gram-stain-positive, terminal-spore-forming bacterium was isolated from an upflow anaerobic filter treating abattoir wastewaters in Tunisia. This strain, designated LIND6LT2T, grew at 40–60 °C (optimum 50–55 °C) and at pH 6.0–8.5 (optimum pH 7.0–7.5). It did not require NaCl for growth, but tolerated it up to 2 %. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as electron acceptors. Growth of LIND6LT2T was inhibited by sulfite (2 mM). Strain LIND6LT2T used cellobiose, glucose, mannose, maltose, mannitol, sucrose and xylose as electron donors. The main fermentation products from glucose metabolism were acetate, formate, butyrate and isobutyrate. The predominant cellular fatty acids were C16 : 0 (68.4 %) and C14 : 0 (8.3 %). The G+C content of the genomic DNA was 35.2 mol%. On the basis of its phylogenetic and physiological properties, a new genus and species, Defluviitalea saccharophila gen. nov., sp. nov., are proposed to accommodate strain LIND6LT2T, placed in Defluviitaleaceae fam. nov. within the phylum Firmicutes, class Clostridia, order Clostridiales. Strain LIND6LT2T ( = DSM 22681T  = JCM 16312T) is the type strain of Defluviitalea saccharophila, which itself is the type species of Defluviitalea.
Stable and dynamic nucleosome states during a meiotic developmental process
Authors: Zhang Liye , Ma Hong , Pugh B. Franklin
Published: April 2011

The plasticity of chromatin organization as chromosomes undergo a full compendium of transactions including DNA replication, recombination, chromatin compaction, and changes in transcription during a developmental program is unknown. We generated genome-wide maps of individual nucleosome organizational states, including positions and occupancy of all nucleosomes, and H3K9 acetylation and H3K4, K36, K79 tri-methylation, during meiotic spore development (gametogenesis) in Saccharomyces. Nucleosome organization was remarkably constant as the genome underwent compaction. However, during an acute meiotic starvation response, nucleosomes were repositioned to alter the accessibility of select transcriptional start sites. Surprisingly, the majority of the meiotic programs did not use this nucleosome repositioning, but was dominated by antisense control. Histone modification states were also remarkably stable, being abundant at specific nucleosome positions at three-quarters of all genes, despite most genes being rarely transcribed. Our findings suggest that, during meiosis, the basic features of genomic chromatin organization are essentially a fixed property of chromosomes, but tweaked in a restricted and program-specific manner.
ABI4 Activates DGAT1 Expression in Arabidopsis Seedlings during Nitrogen Deficiency
Authors: Yang Yang , Yu Xiangchun , Song Lianfen , An Chengcai
Published: April 2011

Triacylglycerol (TAG) is the major seed storage lipid and is important for biofuel and other renewable chemical uses. Acyl-coenzyme A:diacylglycerol acyltransferase1 (DGAT1) is the rate-limiting enzyme in the TAG biosynthesis pathway, but the mechanism of its regulation is unknown. Here, we show that TAG accumulation in Arabidopsis (Arabidopsis thaliana) seedlings increased significantly during nitrogen deprivation (0.1 mm nitrogen) with concomitant induction of genes involved in TAG biosynthesis and accumulation, such as DGAT1 and OLEOSIN1. Nitrogen-deficient seedlings were used to determine the key factors contributing to ectopic TAG accumulation in vegetative tissues. Under low-nitrogen conditions, the phytohormone abscisic acid plays a crucial role in promoting TAG accumulation in Arabidopsis seedlings. Yeast one-hybrid and electrophoretic mobility shift assays demonstrated that ABSCISIC ACID INSENSITIVE4 (ABI4), an important transcriptional factor in the abscisic acid signaling pathway, bound directly to the CE1-like elements (CACCG) present in DGAT1 promoters. Genetic studies also revealed that TAG accumulation and DGAT1 expression were reduced in the abi4 mutant. Taken together, our results indicate that abscisic acid signaling is part of the regulatory machinery governing TAG ectopic accumulation and that ABI4 is essential for the activation of DGAT1 in Arabidopsis seedlings during nitrogen deficiency.
Prediction of Regulatory Interactions from Genome Sequences Using a Biophysical Model for theArabidopsisLEAFY Transcription Factor
Authors: Moyroud Edwige , Minguet Eugenio Gómez , Ott Felix , Yant Levi , Posé David , Monniaux Marie , Blanchet Sandrine , Bastien Olivier , Thévenon Emmanuel , Weigel Detlef , Schmid Markus , Parcy François
Published: April 2011

Despite great advances in sequencing technologies, generating functional information for nonmodel organisms remains a challenge. One solution lies in an improved ability to predict genetic circuits based on primary DNA sequence in combination with detailed knowledge of regulatory proteins that have been characterized in model species. Here, we focus on the LEAFY (LFY) transcription factor, a conserved master regulator of floral development. Starting with biochemical and structural information, we built a biophysical model describing LFY DNA binding specificity in vitro that accurately predicts in vivo LFY binding sites in the Arabidopsis thaliana genome. Applying the model to other plant species, we could follow the evolution of the regulatory relationship between LFY and the AGAMOUS (AG) subfamily of MADS box genes and show that this link predates the divergence between monocots and eudicots. Remarkably, our model succeeds in detecting the connection between LFY and AG homologs despite extensive variation in binding sites. This demonstrates that the cis-element fluidity recently observed in animals also exists in plants, but the challenges it poses can be overcome with predictions grounded in a biophysical model. Therefore, our work opens new avenues to deduce the structure of regulatory networks from mere inspection of genomic sequences.
In Vitro Stimulation and Expansion of Human Tumour‐Reactive CD8+ Cytotoxic T Lymphocytes by Anti‐CD3/CD28/CD137 Magnetic Beads
Authors: Teschner D. , Wenzel G. , Distler E. , Schnürer E. , Theobald M. , Neurauter A. A. , Schjetne K. , Herr W.
Published: April 2011

Adoptive immunotherapy with tumour‐reactive CD8+ cytotoxic T lymphocytes (CTLs) requires efficient in vitro approaches allowing the expansion of CTLs to large numbers prior infusion. Here, we investigated the antigen‐independent activation and the expansion of human T cells in peripheral blood mononuclear cells (PBMCs) and in tumour‐reactive CTLs using Dynabeads coated with monoclonal antibodies to CD3 and to the costimulatory molecules CD28 and CD137 (4‐1BB). T cells in PBMCs showed an increased expansion rate of 15‐ to 17‐fold during a 2‐week culture period using antibody‐conjugated beads with interleukin‐2 (IL‐2) added versus IL‐2 alone. No significant difference between CD3/CD28 beads and CD3/CD28/CD137 beads was observed (P = 0.4). In contrast, expansion of tumour‐reactive CD8+ CTLs over 2 weeks was more efficient using CD3/CD28/CD137 beads (14.4‐fold ±1.2) compared with CD3/CD28 beads (10.6‐fold ±0.7) (P = 0.03) and matched well to the control arm using weekly stimulation with tumour cells. Although all modes of in vitro stimulation decreased the expression of central memory markers CD62L and CCR7 on CTLs, bead‐activated cultures expressed consistently higher levels than tumour‐stimulated cultures. CTLs analysed after bead‐induced expansion versus weekly tumour stimulation showed equal IFN‐γ production in ELISPOT assay. Furthermore, cytotoxicity assays demonstrated an either unchanged or slightly reduced capability of tumour cell lysis for antigen‐independent stimulated CTLs versus those that maintained on weekly tumour stimulation, regardless of which type of beads was used. Our data suggest that the conjugation of anti‐CD137 antibodies to conventional CD3/CD28 beads results in a minor but significant increase in the expansion capacity for tumour‐reactive CD8+ CTLs.
Next‐generation mapping of Arabidopsis genes
Authors: Austin Ryan S. , Vidaurre Danielle , Stamatiou George , Breit Robert , Provart Nicholas J. , Bonetta Dario , Zhang Jianfeng , Fung Pauline , Gong Yunchen , Wang Pauline W. , McCourt Peter , Guttman David S.
Published: April 2011

Next‐generation genomic sequencing technologies have made it possible to directly map mutations responsible for phenotypes of interest via direct sequencing. However, most mapping strategies proposed to date require some prior genetic analysis, which can be very time‐consuming even in genetically tractable organisms. Here we present a de novo method for rapidly and robustly mapping the physical location of EMS mutations by sequencing a small pooled F2 population. This method, called Next Generation Mapping (NGM), uses a chastity statistic to quantify the relative contribution of the parental mutant and mapping lines to each SNP in the pooled F2 population. It then uses this information to objectively localize the candidate mutation based on its exclusive segregation with the mutant parental line. A user‐friendly, web‐based tool for performing NGM analysis is available at http://bar.utoronto.ca/NGM. We used NGM to identify three genes involved in cell‐wall biology in Arabidopsis thaliana, and, in a power analysis, demonstrate success in test mappings using as few as ten F2 lines and a single channel of Illumina Genome Analyzer data. This strategy can easily be applied to other model organisms, and we expect that it will also have utility in crops and any other eukaryote with a completed genome sequence.
Effect of Dietary Fibre on Reproductive Performance of Sows During the First Two Parities
Authors: Che L , Feng D , Wu D , Fang Z , Lin Y , Yan T
Published: April 2011

Contents

The aim of this study was to investigate the effect of dietary fibre on reproductive performance during the first two parities. Gilts were randomly allocated to receive three fibrous diets from days 1–90 of gestation, including low fibre [low fiber (LF), 10.8% neutral detergent fiber (NDF), n = 132], middle fibre [middle fiber (MF), 15.8% NDF, n = 132] and high fibre diet (HF, 20.8% NDF, n = 135), until completion of the second parity. Response criteria included backfat measurements, litter size and pig weight at parturition and day 22 of lactation, weaning‐oestrus‐interval, oestrus rate, sow farrowing and culling rate, uniformity of newborns and relative organ weights. The results showed sows fed LF diet in parity 1 gained more backfat (p < 0.05) during gestation but lost more (p < 0.05) during lactation than sows fed HF diet. Furthermore, sows fed LF diet farrowed more pigs (+0.7–1.1 pigs, p < 0.05) and pigs born alive (+1.0 pigs, p < 0.05) relative to sows fed HF diet. Likewise, sows fed LF and MF diets had greater litter weights at parturition (both p = 0.06) and day 22 after lactation (both p < 0.05). In parity 2, yet, it was MF diet to increase both total pigs born and pigs born alive (+0.9–1.1 pigs, p < 0.05) and litter weight (p = 0.05) relative to other diets. After 22 d of lactation, intriguingly, sows fed HF diet had most pigs alive (p < 0.01–0.07) and heavier litter weight (p = 0.07 or 0.2). Feeding HF diet also increased internal organs weight of newborns (p < 0.05). Collectively, feeding LF and MF diets had beneficial effects on litter weight at parturition and day 22 of lactation in parity 1, and feeding MF diet until parity 2 was able to improve litter size and weight at parturition, but this positive effect disappeared after 22 days of lactation, instead feeding HF diet showed the optimal litter performance.
Comparison of the Effects of Environmental Parameters on Growth Rates of Vibrio vulnificus Biotypes I, II, and III by Culture and Quantitative PCR Analysis
Authors: Chase Eva , Harwood Valerie J.
Published: April 2011

Vibrio vulnificus
is a natural inhabitant of estuarine waters. The three known biotypes include (i) most human pathogens, (ii) primarily eel pathogens, and (iii) pathogens associated with fish and with human wound infections in Israel. Despite the frequently lethal consequences of
V. vulnificus
infections, the growth rates of the various biotypes and their response to environmental changes are not well characterized. We compared the specific growth rates (μ) of a representative of each biotype by culture and quantitative PCR (qPCR) analysis in a defined medium under varied pH, temperature, and salinity. Growth rates based on culturable concentrations were always higher than those based on qPCR estimates; however, both enumeration methods yielded comparable results on the influence of environmental factors on growth rates. Temperature (25°C, 30°C, 37°C), pH (7.0, 8.0), and salinity (5 to 40‰) all had significant effects on the μ of each biotype. Temperature had the greatest effect on the μ of biotype 1 (CMCP6), whereas salinity had the greatest effect on the μ of biotypes 2 (ATCC 33147) and 3 (302/99). The biotypes' growth rates varied significantly; biotype 1 grew most rapidly, while biotype 3 grew most slowly. The highest growth rates were achieved at 37°C, pH 7.0, and salinities of 15 to 30‰ (μ = 4.0, 2.9, and 2.4 generations h
−1
for biotypes 1, 2, and 3, respectively). Other strains of the biotypes yielded comparable results, suggesting that the physiological responses of the biotypes are differentially affected by parameters that are highly variable both in estuarine environments and between the free-living and pathogen states of
V. vulnificus
.
Differing Growth Responses of Major Phylogenetic Groups of Marine Bacteria to Natural Phytoplankton Blooms in the Western North Pacific Ocean
Authors: Tada Yuya , Taniguchi Akito , Nagao Ippei , Miki Takeshi , Uematsu Mitsuo , Tsuda Atsushi , Hamasaki Koji
Published: April 2011

Growth and productivity of phytoplankton substantially change organic matter characteristics, which affect bacterial abundance, productivity, and community structure in aquatic ecosystems. We analyzed bacterial community structures and measured activities inside and outside phytoplankton blooms in the western North Pacific Ocean by using bromodeoxyuridine immunocytochemistry and fluorescence
in situ
hybridization (BIC-FISH).
Roseobacter/Rhodobacter
, SAR11,
Betaproteobacteria
,
Alteromonas
, SAR86, and
Bacteroidetes
responded differently to changes in organic matter supply.
Roseobacter/Rhodobacter
bacteria remained widespread, active, and proliferating despite large fluctuations in organic matter and chlorophyll
a
(Chl-
a
) concentrations. The relative contribution of
Bacteroidetes
to total bacterial production was consistently high. Furthermore, we documented the unexpectedly large contribution of
Alteromonas
to total bacterial production in the bloom. Bacterial abundance, productivity, and growth potential (the proportion of growing cells in a population) were significantly correlated with Chl-
a
and particulate organic carbon concentrations. Canonical correspondence analysis showed that organic matter supply was critical for determining bacterial community structures. The growth potential of each bacterial group as a function of Chl-
a
concentration showed a bell-shaped distribution, indicating an optimal organic matter concentration to promote growth. The growth of
Alteromonas
and
Betaproteobacteria
was especially strongly correlated with organic matter supply. These data elucidate the distinctive ecological role of major bacterial taxa in organic matter cycling during open ocean phytoplankton blooms.