bluuebunny/crossref_metadata_2025 huggingface dataset:
Flexible conformation in organic matter coatings: An hypothesis about soil water repellency
Authors: Roy J. L. , McGill W. B.
Published: April 2011

Some soils develop severe water repellency several years or decades following oil contamination. We previously reported that soil water repellency is completely eliminated by extraction with amphiphilic solvents, but barely reduced by extraction with nonpolar solvents. We report here on solvent-induced reversible soil water repellency. Our results indicate that: (i) water repellency is completely eliminated following extraction with amphiphilic solvent, but partially restored following subsequent exposure to nonpolar, non-H-bonding solvent; (ii) extraction with nonpolar, non-H-bonding solvent generates water repellency in readily wettable control wettable soils, but not in pristine wettable soils, and (iii) repeated sequential extractions alternating between amphiphilic and nonpolar, non-H-bonding solvent increase extractable material and reduce the magnitude of solvent-induced soil water repellency with time.We attribute reversible soil water repellency to solvent-induced changes in the conformation of causative agents of soil water repellency. Recent literature reports on the structural flexibility of "insoluble" organic macromolecules are discussed for supporting evidence. We propose that exposure to nonpolar, non-H-bonding solvents induces stretching of surface-exposed, nonpolar moieties (i.e. alkyl chains), whereas exposure to polar, H-bonding solvents induces their coiling. These solvent-induced conformational changes are retained upon solvent removal. Our results indicate that the wettability of oil-contaminated soils depends on both the interfacial conformation and the fractional coverage of their surface-exposed nonpolar moieties. Key words: Soil water repellency, crude oil, hydrophobic soil, conformational flexibility, swelling, solvents
Effets de deux incorporations d'engrais verts sur le rendement et la nutrition en azote du blé (Triticum aestivum L.), ainsi que sur les propriétés physiques et biologiques du sol
Authors: Abdallahi M. M. , N'Dayegamiye A.
Published: April 2011

The effects of two applications of green manures (1993 and 1995) on soil physical and biological properties, on wheat (Triticum aestivum L.) yields and N uptake were investigated in 1996 in a Le Bras loam (Humic Gleysol). The green manures as main factor were clover (Trifolium pratense L.), buckwheat (Fagapyrum esculentum L.), millet (Sorghum sudanensis L.), mustard (Brassica hirta Moench), colza (Brassica campestris L.) and a control without green manure. The sub-factors consisted of four N fertilizer rates for subsequent wheat: 0, 30, 60 and 90 kg N ha−1. Green manure application significantly increased the soil water stable aggregates (MWD), and the > 0,25 mm fractions of water-stable aggregates (P < 0,05). Levels of soil microbial biomass, alcaline phosphatase and urease activities, and the N mineralization potential were also significantly increased by green manure treatments compared to the control. A 200 to 300% increase in wheat yields and N uptake were obtained, depending on green manure species, compared to the control. The results of this study provide quantitative evidence that wheat yields and N uptake increases were mainly due to N addition into soil and the improvement in soil physical and biological properties by green manure application. Key words: Green manure, wheat yields and N uptake, water stable aggregates, microbial biomass, N mineralization potential, soil enzymes
Using time domain reflectometry in stony forest soil
Authors: Spittlehouse D. L.
Published: April 2011

Forest soils often contain many large coarse fragments making it difficult to insert probes to measure soil water content. The ability of time domain reflectometry (TDR) to give reliable measurements of water content in soil with up to 40% coarse fragments was evaluated at a site in the southern interior of British Columbia, Canada. A commercial time domain reflectometer was used with 0.3-, 0.5- and 0.75-m-long probes to measure soil water content of the profile and layers within the profile. A probe had a shorting diode at the surface and two 3-mm-diameter stainless steel rods inserted vertically, 30 mm apart, as the waveguide. Diverging rods or profile discontinuities resulted in erroneous readings that required a review of the recorded signals and recalculation the travel time. Soil physical and hydrologic soil properties were determined and the soil calibrated for TDR. An accuracy of ±0.02 m3m−3 was obtained with measurement of soil bulk density and minimizing probe and travel time errors. Variation in water content between probes reflected the variability in coarse fragment content; however, the ranking of the probes stayed constant with time and rates of change were similar between probes. One standard deviation on the measured change in the volume of water between measurement days for the 0 to 0.5 m depth was ±6 mm (n = 20), equivalent to 0.012 m3m−3. Measurements of water content of the layers had one standard deviation of 0.02 m3m−3. Key words: Time domain reflectometry, forest hydrology, soil water content, water balance
Quantifying short-term effects of crop rotations on soil organic carbon in southwestern Saskatchewan
Authors: Campbell C. A. , Zentner R. P. , Selles F. , Biederbeck V. O. , McConkey B. G. , Blomert B. , Jefferson P. G.
Published: April 2011

Crop management practices can have a major influence on soil fertility and soil organic C (SOC) sequestration. We need to accurately measure and estimate changes in SOC in the short term (<20 yr). A 10-yr crop rotation experiment, conducted on a medium-textured Orthic Brown Chernozem at Swift Current, in southwestern Saskatchewan, was sampled in 1990 (3 yr after initiation of the study) and in 1993 and 1996, to measure SOC changes under nine crop rotation treatments. Minimum tillage practices were used. The stubble was cut high to enhance snow trap and N and P fertilizer applied based on soil tests. Grain and straw yields of the cereals, and hay yields of the crested wheatgrass (CWG) [Agropyron cristatum (L.) Gaeertn.] were measured annually. An empirical equation which uses two simultaneous first order kinetic expressions, one to estimate crop residue decomposition and the other to estimate soil humus C mineralization was used, together with crop residue (straw and estimated root) C inputs, to estimate SOC changes over the 1987 to 1996 period. The estimated SOC values for the 1990 to 1996 period were generally similar to the measured values (r2 = 0.64, P < 0.0001). Significant (P < 0.10) changes in SOC were not observed below 15 cm depth, perhaps because shallow tillage (10- to 12.5-cm depth) is practiced. A change from cropland to CWG did not increase SOC, and this treatment, chemical fallow-winter wheat (Triticum aestivum L.)-spring wheat (F-WW-W), and F-high-yielding (Hy) Canada Prairie Spring (CPS) wheat-Hy (F-Hy-Hy) rotations, had the lowest SOC gains among the rotations. The CPS wheat had a higher harvest index (0.46) than hard red spring (HRS) wheat (0.39), but it increased SOC less than the comparable HRS wheat rotation between 1990 and 1996 indicating that higher grain yields do not always equate to higher SOC. Weather conditions were favourable for cereals from 1990 to 1996 and we measured significant increases in SOC (up to 5.5 Mg ha−1 in 6 yr). This is encouraging for producers who may be contemplating participating in "C trading", although this also suggests that periods of less favourable weather will limit gains in SOC. Summerfallowing once in 4 yr in this semiarid environment did not reduce SOC gains compared to continuous wheat (Cont W). For example, a F-W-W-W rotation gained 4.88 Mg C ha−1 in 6 yr while continuous wheat gained 5 Mg ha−1. Growing Indianhead lentil (Lens culinaris Medikus) as a legume green manure crop (GM) with wheat in a GM-W-W rotation did not increase SOC more than F-W-W. The efficiencies of conversion of residue C to SOC were high, ranging between 9% for frequently fallowed systems to 29% for continuously cropped systems, likely due to the favourable weather conditions experienced. Key words: Carbon sequestration, legume green manure, crested wheatgrass, harvest index effect, C conversion efficiencies
Phosphorus release from coated monoammonium phosphate: Effect of coating thickness, temperature, elution medium, soil moisture and placement method
Authors: Zhang Mingchu , Nyborg M. , Malhi S. S. , McKenzie R. H. , Solberg E.
Published: April 2011

Coating fertilizer granules with a polymer slows the release of nutrients over a long period of time, so that the fertilizer uptake by plants may be enhanced. Two laboratory experiments were conducted to determine the effects of coating thickness, temperature, soil moisture, and placement method on the release rate of P from coated monoammonium phosphate (MAP) in soil; to compare the release rate of P from coated MAP in soil and in water; and to evaluate different kinetic equations for simulating the release of P from coated MAP. In exp. 1, release of P from 10 pre-weighed granules of a non-coated MAP and three polymer-coated MAP fertilizers (Coated I, 4%; Coated II, 4.5%; and Coated III, 5%) was determined in water at 10 and 23°C. In exp. 2, release of P from the four MAP fertilizers in soil was determined at two temperatures (10 and 23°C), two moisture levels (90 and 60% field capacity) and two placement methods (incorporation and banding). Four kinetic equations, i.e., simple Elovich, Parabolic diffusion, Power function, and First order kinetics, were evaluated to simulate the release of P from coated MAP. Activation energy of P release was calculated using the P release versus ln time plots of the simple Elovich equation. The release rate of P from coated MAP was strongly affected by coating thickness and temperature but was not affected by method of P placement and soil water content. The release of P from coated MAP was slower in soil than in water, and it decreased markedly with increasing thickness of polymer coating on MAP, whereas it increased with increasing temperature. The simple Elovich equation best described the release of P from coated MAP in both water and soil. The activation energy was not affected by elution medium and coating thickness but it was lower at the higher temperature. In conclusion, the test of P release rate from coated MAP in water may not represent the true release rate of P from coated MAP in soil, as it is influenced by elution medium, temperature and coating thickness. The simple Elovich equation best described the P release kinetics from coated MAP in soil and in water. Key words: Coating thickness, monoammonium phosphate, P release rate in water and soil, P release kinetics, placement method, soil moisture content, temperature
Use of ion exchange membrane to assess soil N supply to canola as affected by addition of liquid swine manure and urea
Authors: Qian P. , Schoenau J. J.
Published: April 2011

A growth chamber study was conducted using two Saskatchewan soils to evaluate how addition of urea and swine manure affects the supply of plant-available nitrogen (ammonium and nitrate) and its relationship with plant N uptake. Treatments consisted of two different N rates applied as urea and manure (100 and 800 mg N kg−1) and a control. Ion exchange membrane probes were used to measure plant-available N supply rate. Canola was grown under the same environmental conditions to determine plant N uptake. Additions of fertilizer and manure significantly increased the supply of plant-available N measured in the soil. Over an 84-d period the available N supply in the manured soil was about 40% lower than in the urea-fertilized soil at equivalent rates of total N addition due to incomplete mineralization of organic N in the manure. However, plant N uptake was similar between manure and urea-treated soils, which was attributed to other nutrients present in the manure that may have enhanced root growth and plant N uptake. High proportions of ammonium N were measured initially, especially at the high rates of urea and manure. However, inorganic N in the form of ammonium rapidly decreased with time and nitrate N became the main inorganic N form supplied. Overall, there was good correlation (r value 0.79 to 0.96) between plant N uptake and available N supply rate in the soil as measured by ion exchange membrane. Key words: Ion exchange membrane, available N supply rate, urea, swine manure, canola, plant N uptake
Catalytically enhanced spectrophotometric determination of manganese in seawater by flow‐injection analysis with a commercially available resin for on‐line preconcentration
Authors: Aguilar‐Islas Ana M. , Resing Joseph A. , Bruland Kenneth W.
Published: April 2011

The sensitive, laboratory‐ and ship‐based, flow‐injection (FI) method for the determination of dissolved manganese in seawater developed by Resing and Mottl (Anal. Chem. 1992;64:2682‐2687) has been significantly modified and improved by incorporating five significant changes. The three major changes are the use of a commercially available iminodiacetate (IDA) resin (Toyopearl AF‐chelate 650M) in place of 8‐hydroxyquinoline for on‐line preconcentration of manganese and matrix removal, the addition of nitrilotriacetic acid as an activator ligand which increases sensitivity by a factor of 7 and decreases the limit of detection, and the on‐line buffering of acidified samples before column loading. Two minor improvements include use of the more soluble sodium periodate in place of potassium periodate and elimination of Brij‐35 surfactant. To accommodate these changes, the pH of samples was adjusted to 8.5 (vs. 7.8), a higher acid concentration was required to elute the Mn from the IDA resin, and stronger reaction buffer was required to neutralize the acid. The accuracy of the method was evaluated with the use of NASS‐4 standard seawater and by a comparison study of samples from the California coast that were analyzed by this method and an FI method coupled to inductively coupled plasma sector field mass spectrometry detection. The detection limit and precision of the method depend on the amount of sample preconcentrated onto the column. By preconcentrating 1.6 mL of sample, a detection limit of 0.03 nM (3 times the standard deviation of a blank) and precision of 3.2% (as percent relative standard deviation) were obtained. The method was used on board ship to determine dissolved manganese in coastal waters off Oregon and Washington.
A new method for estimating growth rates of alkenone‐producing haptophytes
Authors: Popp Brian N. , Bidigare Robert R. , Deschenes Bryan , Laws Edward A. , Prahl Fredrick G. , Tanimoto Jamie K. , Wallsgrove Richard J.
Published: April 2011

Laboratory culture experiments were performed to establish the range of growth conditions where 13C labeling of di‐ and tri‐unsaturated C37 methyl ketones yields reliable growth rates for alkenone‐producing algae. Results document that even at low growth rates and short time intervals, 13C labeling of the di‐unsaturated C37 alkenone provides reasonable estimates of growth rate for Isochrysis galbana, Isochrysis sp., and three strains of Emiliania huxleyi. These findings suggest that although alkenone biosynthesis almost certainly involves a complex combination of intermediate pools, those pools must turn over at a rate sufficiently fast that the labeling of the di‐unsaturated C37 alkenone is not greatly biased. However, bias was noted for the tri‐unsaturated alkenone, suggesting that either growth rates in the field should be based on K37:2 labeling or that long incubations should be used. Specific growth rates calculated from alkenone 13C labeling experiments conducted in the subarctic Pacific decreased as a function of depth in the euphotic zone and were linearly correlated with photosynthetically active radiation below ~50 µEin m−2 s−1. These observations indicate that at depths greater than ~25 m, growth rates of the alkenone‐producing algae were light‐limited. Determination of the specific growth rates of the alkenone‐producing algae was motivated by our present knowledge of the controls on stable carbon isotopic fractionation in marine microalgae. Development of our alkenone 13C labeling technique for in situ growth rate determinations allows evaluation of the effect of growth rate on carbon isotopic fractionation in natural populations of E. huxleyi and Gephyrocapsa oceanica so that laboratory‐based microalgal stable isotope fractionation hypotheses may be evaluated in the field.
Particle tracking in a salinity gradient: A method for measuring sinking rate of individual phytoplankton in the laboratory
Authors: O'Brien Katherine R. , Waite Anya M. , Alexander Bridget L. , Perry Karen A. , Neumann Luis E.
Published: April 2011

This paper presents a new method to measure the sinking rates of individual phytoplankton “particles” (cells, chains, colonies, and aggregates) in the laboratory. Conventional particle tracking and high resolution video imaging were used to measure particle sinking rates and particle size. The stabilizing force of a very mild linear salinity gradient (1 ppt over 15 cm) prevented the formation of convection currents in the laboratory settling chamber. Whereas bulk settling methods such as SETCOL provide a single value of sinking rate for a population, this method allows the measurement of sinking rate and particle size for a large number of individual particles or phytoplankton within a population. The method has applications where sinking rates vary within a population, or where sinking rate‐size relationships are important. Preliminary data from experiments with both laboratory and field samples of marine phytoplankton are presented here to illustrate the use of the technique, its applications, and limitations. Whereas this paper deals only with sinking phytoplankton, the method is equally valid for positively buoyant species, as well as nonbiological particles.
Effect of different sampling designs and methods on the estimation of secondary production: A simulation
Authors: Cusson Mathieu , Plante Jean‐François , Genest Christian
Published: April 2011

This article reports the results of a simulation study designed to investigate the effect of several sampling design factors on the accuracy and precision of various estimates of secondary production. Whereas most previous studies of this sort were concerned with freshwater fauna (e.g., insects), the hypothetical population used here reflects the characteristics of marine mussels from cold‐temperate and subarctic regions. It features the simultaneous presence of different cohorts, gradual recruit arrival, seasonal growth oscillation, and quadratdependent population density, as well as random individual variation both in survival and in weight gain. For this population, the percentage relative bias (PRB) and relative root mean squared error (RRMSE) of 4 classic cohort‐based methods, 3 size‐based methods, and several variants thereof were computed as a function of sampling frequency, distribution of sampling dates, number of quadrats sampled per occasion, inclusion or omission of the last sampling date, and coarseness of the size classes and sieve aperture. Although most methods performed reasonably well, non‐negligible differences were observed among them. A version of Allen's curve technique and a mass‐specific growth rate method gave the best results for cohort‐ and size‐based method groups, respectively. Sampling effort, in terms of both frequency of sampling and number of samples per date, had the largest documented influence on both PRB and RRMSE. Recommendations are made for the best compromises between methods and sampling designs to achieve reliable production estimates for populations with similar characteristics.
Microcosm design and evaluation to study stream microbial biofilms
Authors: Singer Gabriel , Besemer Katharina , Hödl Iris , Chlup Annkatrin , Hochedlinger Gerald , Stadler Peter , Battin Tom J.
Published: April 2011

Biofilms represent the dominant form of microbial life in stream ecosystems. Research of complex environmental biofilms requires appropriate cultivation techniques to address questions central to biofilm structure‐function‐coupling and ecosystem implications. Whereas the cultivation of medical and industrial biofilms has received considerable attention, cultivation devices for environmental biofilms have not. Here we describe and systematically assess the reproducibility of laboratory‐based microcosms that allow the study of the structure and function of stream biofilms under different flow regimes. Microcosms were assembled from 1.3‐m‐long Plexiglas flumes fed with water that recirculated between a header tank and a sink. Each flume was paved with 104 individual unglazed ceramic coupons that served as growth substratum. We operated 3 microcosms designed to simulate laminar, transitional, and turbulent flow. Each microcosm consisted of two duplicate sets of flumes where two flumes shared the same water. We monitored biofilm coverage, bacterial abundance, and chlorophyll a as bulk biomass parameters over a growth period of 28 days and tested for community composition shifts using denaturing gradient gel electrophoresis (DGGE). Based on these variables, we assessed the reproducibility at different levels of microcosm assembly: (1) within individual flumes (i.e., longitudinal gradients), (2) within a shared water body, and (3) within flow regime treatments. Our results revealed good reproducibility at the various levels of the experimental setup and suggest microcosm flumes as highly valuable tools for biofilm studies with multitreatment and multireference designs.
Low dissolved DMSP concentrations in seawater revealed by small‐volume gravity filtration and dialysis sampling
Authors: Kiene Ronald P. , Slezak Doris
Published: April 2011

A variety of filtration and passive dialysis protocols were tested with seawater for determination of the dissolved concentrations of dimethylsulfoniopropionate (DMSPd), a compound originating in the cytosol of many marine phytoplankton. Commonly used sampling procedures, such as in‐line filtration, syringe pressure filtration, and gravity filtration of relatively large‐volume samples (5‐50 mL) through glass fiber filters, caused release of DMSPd from particulate material as evidenced by increasing DMSPd concentrations with volume filtered. Exposure of filters to air at the end of filtration caused particularly severe DMSPd release. Dialysis bags or Slide‐A‐Lyzer dialysis cassettes equilibrated with seawater DMSPd within 4 h, even in polar waters (−1.8 °C), and appeared to give accurate DMSPd concentrations in some circumstances. However, incubation of seawater in laboratory containers (e.g., glass jars) during dialysis sometimes caused artifactual release of DMSPd. We therefore adopted a small‐volume gravity drip filtration (SVDF) procedure, the essential elements of which were: (i) collection of 20 to 50 mL seawater directly from the primary sample container (e.g., Niskin bottle) into a dry, all‐plastic filtration tower; (ii) use of a 47‐mm‐diameter Whatman GF/F filter; (iii) rapid (< 3 min) filtration by gravity (hydrostatic) pressure; (iv) collection of only the first 3.5 mL filtrate for DMSPd analysis; and (v) never exposing the filtered plankton to air. The SVDF procedure appeared to yield the same low DMSPd concentrations as dialysis samplers incubated in the ocean water column. Using the SVDF procedure, DMSPd was found to be < 2.8 nM over a broad range of ocean water types and particulate DMSP concentrations. The maximum DMSPd concentration observed in our study (2.8 nM) was far lower than the reported worldwide average DMSPd concentration of 16.9 nM, raising the possibility that past data collections may have been influenced by filtration artifacts.
Near‐infrared spectrometry (NIRS) for the analysis of seston carbon, nitrogen, and phosphorus from diverse sources
Authors: Hood James M. , Brovold Sandy , Sterner Robert W. , Villar‐Argaiz Manuel , Zimmer Kyle D.
Published: April 2011

Seston carbon (C), nitrogen (N), and phosphorus (P) concentrations are routinely measured by limnologists and oceanographers. Unfortunately, common methods for the determination of seston C, N, and P are expensive and labor intensive and result in sample destruction. It has been suggested that near‐infrared spectroscopy (NIRS) may be preferable to primary chemical analyses because NIRS is rapid and nondestructive. The ability of NIRS to measure seston element concentrations has been demonstrated, but an impediment to widespread adaptation of this technique relates to the generality of prediction (i.e., standard) equations. For diverse environmental samples, the ability to develop one global predictive equation is important, since the calibration process involves a considerable investment. It is unclear how often during routine use an investigator must standardize and calibrate NIRS equations. Here we explore the use of NIRS for analysis of seston C, N, and P in diverse aquatic samples, including those from monocultures, Lake Superior, and two sets of numerous lakes and ponds. Predictive equations were developed for specific datasets and for all the datasets combined (global equation). In most cases dataset‐specific equations and the global equation accurately predicted (R2 > 0.90) concentrations of seston C and N but not P. Prediction error varied among seston types and increased when equations were tested on novel datasets. Our results indicate that NIRS analysis is an effective alternative to primary C and N chemistry, particularly for large aquatic monitoring programs. However, care must be taken during calibration and routine use, as accuracy depends on the types of seston in the calibration dataset.
Determination of the particulate absorption of microalgae using a point‐source integrating‐cavity absorption meter: verification with a photometric technique, improvements for pigment bleaching, and correction for chlorophyll fluorescence
Authors: Röttgers Rüdiger , Häse Clivia , Doerffer Roland
Published: April 2011

The determination of the spectral light absorption coefficient of planktonic algae in seawater is crucial for many applications, including optical remote sensing. Common techniques are adversely affected by light‐scattering effects, or by low particle concentrations in situ. Measurements with a point‐source integrating‐cavity absorption meter (PSICAM) can overcome both difficulties. In our study, we assessed the performance of a PSICAM for measuring the absorption coefficients of microalgae by a comparison with state‐of‐the‐art techniques. The PSICAM was evaluated by comparative measurements of diluted algal cultures with a photometric setup, where the sample cuvette is placed in the center of an integrating sphere (CIS). The accuracy of both the CIS and the PSICAM technique was calibrated against a commercial spectrophotometer by measurements of dense algal cultures. The remaining sources of error for the PSICAM technique were the bleaching procedure and chlorophyll fluorescence. We propose an improved bleaching technique and introduce a correction procedure for the fluorescence effects. Applying both, the overall differences between PSICAM and CIS measurements were less than ± 1%. We further demonstrate that the accuracy of the PSICAM is at least as good as that of a commercial spectrophotometer, but its precision should be two to three orders of magnitude higher. Due to its high sensitivity and accuracy, and to the fact that sources of error can be identified and accounted for, the PSICAM has a great potential to significantly improve the determination of absorption spectra of particulate matter in natural seawater.
In situ pore water sampling in deep intertidal flat sediments
Authors: Beck Melanie , Dellwig Olaf , Kolditz Kerstin , Freund Holger , Liebezeit Gerd , Schnetger Bernhard , Brumsack Hans‐Jürgen
Published: April 2011

In this study, we present a multilevel in situ pore water sampler that allows pore water sampling down to 5 m sediment depth. The sampler forms a crucial tool to study biogeochemical processes on different time scales in advective pore water systems. After insertion into the sediment, the sampler stays on site, allowing repetitive sampling at identical locations and depth intervals. The sampler has been successfully tested for 1 year in sandy sediments in the backbarrier tidal flats of Spiekeroog Island at the German North Sea coast. Depth profiles of redox‐sensitive elements show a high depth resolution and are not affected by oxidation artifacts during extraction. Seasonal variations because of advection and changing microbial activity are apparent for some element species even at sediment depths of 5 m.
Culturing the marine cyanobacterium Prochlorococcus
Authors: Moore Lisa R. , Coe Allison , Zinser Erik R. , Saito Mak A. , Sullivan Matthew B. , Lindell Debbie , Frois‐Moniz Katya , Waterbury John , Chisholm Sallie W.
Published: April 2011

Prochlorococcus is the numerically dominant primary producer in open ocean ecosystems. Analysis of Prochlorococcus genome sequences from cultured isolates and ocean samples has broadened interest in studying this tiny cell, and efforts are underway to develop it into a model system for studying marine microbial ecology. A critical component of these efforts has been the development of systematic culturing methods that will facilitate the distribution of Prochlorococcus to diverse labs that may be interested in studying it. This paper provides detailed methods for maintaining cultures of Prochlorococcus, including a comparison of growth rates of cells on two artificial seawater media and on a standard medium that uses a natural seawater base. Procedures for agar plating, cryopreservation, obtaining new isolates, and issues associated with culture volume and carbon limitation also are described.
Partitioning total spectral absorption in phytoplankton and colored detrital material contributions
Authors: Oubelkheir Kadija , Claustre Hervé , Bricaud Annick , Babin Marcel
Published: April 2011

A method based on spectral information is used to derive spectral absorption coefficients of phytoplankton aφ(λ) and colored detrital material, CDM, which includes non‐algal particle and colored dissolved organic matter, aCDM(λ), from total minus water absorption coefficients measurements. This method is first validated over a dataset of more than 300 simultaneous measurements of phytoplankton, non‐algal particle, and colored dissolved organic matter absorption coefficients spectra acquired with a laboratory spectrophotometer in various oceanic and coastal European waters. The validation is presented for measurements made with a high spectral resolution (hyper‐spectral case), and a limited spectral resolution (multi‐spectral case) — the case of most devices routinely used for in situ profiling, such as the WETLabs ac‐9. In order to examine the various sources of error in the method, we test its performance considering various levels of a priori knowledge of phytoplankton absorption properties over the study area: for each site, over each region, or over a global dataset only. When the method is applied to the multi‐spectral case without introducing any “local” information on phytoplankton absorption properties, we obtain a good performance with a relative Root Mean Square Error equal to 17.8%, 14.6%, and 40.7% for aCDM(412), the CDM exponential slope, and aφ(440), respectively. Finally, the partitioning method is directly applied to in situ profiles of total minus water spectral absorption coefficient measured with an ac‐9 in various oceanic Mediterranean waters, allowing the in situ description of CDM and phytoplankton absorption coefficients with a high spatial resolution.
LISST‐100 measurements of phytoplankton size distribution: evaluation of the effects of cell shape
Authors: Karp‐Boss Lee , Azevedo Laura , Boss Emmanuel
Published: April 2011

Information on cell size is central to studies of phytoplankton ecology, yet in situ measurements of particle size distribution remain a challenge. The LISST‐100 (Laser In Situ Scattering and Transmissometry; Sequoia Scientific, Inc.) is one of few commercially available instruments that provide autonomous measurements of size distributions of suspended particles in situ. Its capability to size phytoplankton needs to be evaluated, however, for two reasons. First, size is not measured directly; rather, information on size is obtained from near‐forward scattering measurements that are inverted to obtain size distributions. The inversion assumes that particles are homogeneous spheres. Phytoplankton, however, display a wide range of cell shapes and their scattering behavior is likely to be different from that of spheres. Second, the LISST‐100 was originally designed for sediments and its inversion assumes an index of refraction typical of inorganic particles. We compared size and volume concentration distributions obtained by the LISST‐100 to those derived via microscopy for phytoplankton cultures of different cell sizes and shapes. Results demonstrate the success of the LISST‐100 in measuring size and volume concentrations of cells with a cell aspect ratio that is close to 1 and illustrate its limitations when nonspherical cells are present in the sample. Uses of the LISST‐100 in laboratory and field studies are discussed in light of the results from this study.
An empirical algorithm for determining the diffuse attenuation coefficient Kd in clear and turbid waters from spectral remote sensing reflectance
Authors: Zhang Tinglu , Fell Frank
Published: April 2011

A robust empirical algorithm to determine the diffuse attenuation coefficient Kd at a wavelength of 490 nm (Kd490) from spectral remote sensing reflectance has been derived from the NOMAD data set and tested against the COASTLOOC data set. Together, both data sets contain more than 3,800 observations of concomitantly acquired bio‐optical parameters in waters ranging from very clear to very turbid, of which about 2,300 have been used in this study. The proposed algorithm follows a power law of the form Kd490 = 10^(a0 + a1 x + a2 x2 + a3 x3) + a4, where x is the common logarithm of either of two remote sensing reflectance ratios: log10 (Rrs490/Rrs555) for clear waters and log10 (Rrs490/Rrs665) for turbid waters. Switching between the ratios is triggered when Rrs490/Rrs555 drops below a threshold value of 0.85 corresponding to a Kd490 value of approx. 0.2 m−1. Our algorithm shows comparable performance in both clear and turbid waters. Due to its simplicity and the public availability of the underlying in situ data, localization of the algorithm by appropriate sub‐setting of the NOMAD data and/or adding other in situ data are straightforward.
Calibrating the Dynamic Reservoir Simulation Model (DYRESM) and filling required data gaps for one‐dimensional thermal profile predictions in a boreal lake
Authors: Tanentzap Andrew J. , Hamilton David P. , Yan Norman D.
Published: April 2011

One‐dimensional vertical heat transfer and mixing models, such as the Dynamic Reservoir Simulation Model (DYRESM), have seldom been applied to lakes in the boreal region even though this region houses the majority of global freshwater lakes. In order to employ DYRESM to predict the thermal structure of a boreal lake located near Sudbury, Ontario, Canada, we overcame two methodological challenges. First, we developed models to predict the vertical light extinction coefficient (Kd) from dissolved organic carbon (DOC) concentrations and hydraulic retention time. We also developed models to predict stream temperatures from local meteorology, and to predict the discharge of lake inflows and the lake outflow from runoff per unit area at gauged streams nearby. We then re‐calibrated several DYRESM parameters which had been tested previously primarily in the Southern Hemisphere, and explored the sensitivity of the re‐calibrated model to all of the remaining uncalibrated inputs implicated in heating and mixing processes. The mean difference between values predicted with the re‐calibrated model and field measurements (± 1 standard deviation), 1.09 m (± 0.89 m) for thermocline depth and 1.98°C (± 1.58°C) for bottom water temperature, was relatively small compared with other North American studies, and likely due to the model rather than our parameterization. Our calibration of DYRESM for Clearwater Lake, and supplementary models, provide a demonstration for and guidance to those wishing to simulate changes in thermal regimes of boreal lakes in response to climate change or other broad‐scale environmental stressors of importance both to local fisheries and freshwater resource management.
Estimating in situ phytoplankton growth rates with a Lagrangian sampling strategy
Authors: Hillmer Ingrid , Imberger Jörg
Published: April 2011

Quantification of biogeochemical rates is essential to the understanding of the dynamics of aquatic ecosystems. However, this has proven to be difficult to achieve especially under conditions of high spatial and temporal hydrodynamic and biogeochemical variability. Here, a Lagrangian experimental design was employed to estimate biogeochemical rate coefficients in situ. A set of four drogues and a cross‐transect sampling design was used to capture the patchy distribution of phytoplankton and nutrient species, and high transport and mixing rates. A mass balance approach was applied to a Lagrangian control volume moving with a drogue. This approach was used to separate internal biogeochemical changes from the physical changes due to advection, diffusion, and convergence/divergence fluxes. This experimental approach was applied to an oligotrophic coastal region. The phytoplankton growth rate, primary production, and carbon to chlorophyll ratio (C:Chla) obtained from the experiment agreed with the highest literature values for this study site. This supported the validity of this approach. The effect of scales of processes and patchiness is highlighted from this experiment. It is shown that the experimental design is subject to a relationship between size of the control volume, the time scale of internal processes, and sampling time.
Fluid displacive resin embedding of laminated sediments: preserving trace metals for high‐resolution paleoclimate investigations
Authors: Jilbert Tom , de Lange Gert , Reichart Gert‐Jan
Published: April 2011

For the high‐resolution study of trace metal profiles in laminated anoxic sediments, a specially adapted method of resin embedding has been developed. Fluid displacement is the preferred means of sediment dehydration, offering optimum structural preservation and facilitating desalination. Exchanges of deionized water, acetone, and low‐viscosity resin are performed in an oxygen‐deficient atmosphere to maintain anoxia in the sediments. Analysis of the rinsing fluids indicates both efficient removal of brine salts and minimal dissolution of redox‐sensitive trace metals. This contrasts with oxic fluid displacement experiments, in which several metals appear to be removed from the solid phase during desalination. Laser Ablation‐Inductively Coupled Plasma‐Mass Spectrometry (LA‐ICP‐MS) scanning of the embedded blocks shows that the adapted preparation viably preserves both the redox‐sensitive chemistry and physical structure of the sediment.
Naturally present fatty acids as internal calibrants for Fourier transform mass spectra of dissolved organic matter
Authors: Sleighter Rachel L. , McKee Georgina A. , Liu Zhanfei , Hatcher Patrick G.
Published: April 2011

The analysis of dissolved organic matter (DOM) by Fourier transform ion cyclotron resonance mass spectrometry (FTICR‐MS) has gained wide interest recently, driven primarily by its ultrahigh resolving power and mass accuracy. Accurate calibration of mass spectra is a key step to successfully decipher the DOM components. We propose a simple and accurate method to internally calibrate the peaks in the complex spectra without the need to add a calibrant. Mass spectra of DOM samples from the Dismal Swamp, Virginia, and the lower Chesapeake Bay display the presence of naturally occurring fatty acids which can be readily recognized and calibrated with accuracies <0.1 ppm. Once calibrated with fatty acids, approximately 80% of all peaks in the DOM mass spectra can be assigned unique molecular formulas with accuracies <0.4 ppm. Although the formula errors for the assigned molecular formulas do increase with increasing m/z, the dynamic range of the fatty acids used as calibrants is sufficient because high m/z values (>600) have formulas with an average error of <0.6 ppm. Because fatty acids are ubiquitous components of most DOM, this approach is applicable to a large variety of DOM samples.
Porous underwater chamber (PUC) for in‐situ determination of nutrient and pollutant bioavailability to microorganisms
Authors: Hassler Christel S. , Twiss Michael R. , Simon Dana F. , Wilkinson Kevin J.
Published: April 2011

Physical (e.g., temperature and light) and biogeochemical (e.g., cycling) parameters are known to affect bioavailability and toxicity of nutrients and pollutants to microorganisms. A system that would allow exposure of selected microorganisms to in situ conditions could provide relevant and novel evaluations of bioavailability. A simple and low cost 37 mL porous underwater chamber (PUC), in which test microorganisms are exposed to field conditions, is presented. The PUC is a thin, acrylic cylinder with polycarbonate membranes on each side, providing an optimal (75 cm2) exchange with the external solution. Regardless of the membrane pore size (0.4 and 5 µm), the PUC required 10 h to equilibrate with the external solution, close to the theoretical time determined for the diffusion of a model compound, the Suwannee River fulvic acid. For in situ use, the PUCs can be filled with filtered water to minimize the equilibration time. The system was validated in 20 to 60 L artificial freshwater by evaluating (1) Cd bioaccumulation by the microalga Chlamydomonas reinhardtii and (2) iron bioavailability to a cyanobacterial bioreporter in comparison with conventional bottle assays. The use of the PUC resulted in no significant differences in Cd uptake fluxes or iron bioavailability. Field experiments undertaken on Lake Erie demonstrated that the PUCs could be used to evaluate the contribution of particulate iron to iron bioavailability. Because the PUCs might not correctly reflect bioavailability for substances at low concentrations with high biouptake fluxes, a critical discussion with respect on the rate‐limiting steps of the device is presented. Several considerations that might facilitate the appropriate use of the PUCs are given.
The NEREUS in‐lake wireless/acoustic chemical data network
Authors: Hemond Harry , Cheung Jimmy , Mueller Amy , Wong Joseph , Hemond Michael , Mueller Daniel , Eskesen Justin
Published: April 2011

We describe a system for the semi‐autonomous in situ measurement of lake chemical properties, with high temporal resolution and the potential to map chemical properties in 3 dimensions. The system comprises both fixed sensor locations on moored buoys and one (or potentially more) autonomous underwater vehicles (AUVs) serving as mobile underwater sensor platforms. Sensors include conventional water quality multiprobes and thermistor strings and the NEREUS underwater mass spectrometer for measurement of dissolved metabolic gases such as methane as well as permanent gases. Data are delivered to a shore station via a network that includes acoustic modems for communication with the AUV and a radio network operating in the license‐free ISM (industrial, scientific, and medical) band operating under the IEEE 802.11b protocol. The system is designed to use low‐cost commercial hardware and open‐source software wherever possible. We constructed a prototype system of 3 buoys, 1 AUV, and a shore station, and field tests have demonstrated its ability to measure and remotely display lake chemical data in real time.
Underway monitoring of nanomolar nitrate plus nitrite and phosphate in oligotrophic seawater
Authors: Li Qian P. , Hansell Dennis A. , Zhang Jia‐Zhong
Published: April 2011

To study nutrient dynamics and cycling in oligotrophic open ocean environments, continuous measurements of nanomolar nitrate, nitrite, and phosphate are valuable. However, such studies are usually impeded by the detection limits of conventional nutrient‐sensors and analyzers. Here, we developed a shipboard deployable underway system for simultaneously monitoring nitrate plus nitrite and phosphate at nanomolar concentrations by the coupling of an optimized flow injection analytical system with two long‐path liquid waveguide capillary cells (LWCC). The detection limits are ~2 nM for nitrate plus nitrite and ~1.5 nM for phosphate, respectively. Results from realtime surveys of waters over the west Florida continental shelf and the oligotrophic Sargasso Sea are presented. This system has also been successfully used to analyze more than 1000 discrete seawater samples manually during 2 cruises in the North Atlantic.
Development and initial deployments of an autonomous in situ instrument for long‐term monitoring of copper (II) in the marine environment
Authors: Holm Christopher E. , Chase Zanna , Jannasch Hans W. , Johnson Kenneth S.
Published: April 2011

We developed an autonomous, in situ instrument to detect dissolved copper in seawater, suitable for deployment on time scales from weeks to a month. A commercially available in situ nitrate analyzer (YSI 9600) was adapted to measure copper (II) by chemiluminescence. Modifications included construction of a photomultiplier (PMT)—based detector and flow‐cell, the use of more chemically resistant plastics for parts in contact with the reagents, addition of an online acidification step, and optimization of the method and flow parameters. Microsolenoid pumps take in sample and dispense reagent, standard, and blank solutions, which are stored in 1 L plastic bags. Filtration (0.45 µm) and acidification (pH ~1.7) permit a measurement of total dissolved Cu(II). Calibration is achieved by periodically analyzing ligand‐stabilized seawater standard and blank solutions stored at pH 8 and acidified online. Averaged over all in situ deployments, the instrument had a detection limit of 0.8 ± 0.3 nM, a sample precision of 11% (n = 612), and an accuracy of 17% (compared to discrete samples n = 27). The instrument is capable of functioning autonomously for 25 d when sampling every hour and calibrating every 6 h. Reagent consumption is the limiting factor.
P‐affinity measurements of specific osmotroph populations using cell‐sorting flow cytometry
Authors: Larsen Aud , Tanaka Tsuneo , Zubkov Mikhail V. , Thingstad T. Frede
Published: April 2011

To elucidate the role that the marine microbes play in global nutrient cycling, it is necessary to recognize how various phyto‐ and bacterioplankton groups compete for limiting nutrients. Specific phosphate affinity describes an organism's ability to harvest phosphate at low concentrations from the surrounding water. For the first time, we have taken advantage of cell‐sorting flow cytometry in combination with radio‐labeled phosphorus to measure this feature of specific osmotrophic groups in natural communities. Specific phosphate affinities for Synechococcus spp. and picoeukaryotes were measured using live, unstained cells. The results were always lower than theoretical calculated maximum values, corresponding well with observations of P‐deficiency, or sub‐optimal P supply for the osmotroph community, at the time of investigation. Fixing and staining cells before flow sorting offers the advantage of better separation of phytoplankton and showed high sorting reproducibility when applied to nonaxenic Synechococcus cultures. A subsequent investigation of P‐leakage from isotopically labeled, fixed, stained cells in nonaxenic cultures of Synechococcus showed that it was only slightly larger than the loss of 17% found when uptake of new label was stopped with adding “cold” phosphate. Possible applications of the currently developed methodology for population specific P affinity measurements by flow sorting are discussed.