bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated measurements of filamentous cyanobacteria by digital image analysis
Authors: Almesjö Lisa , Rolff Carl
Published: April 2011

Abundance and biomass estimations of filamentous cyanobacteria often use conventional microscope measurements, which are highly time‐consuming and provide no information on filament morphology. In this article, we describe an image analysis method developed for rapid, semiautomated or fully automated estimations of filament lengths and abundance of uncoiled cyanobacteria. The method was developed for the Baltic Sea cyanobacterium Aphanizomenon sp. and then applied on Trichodesmium sp. strain IMS101 to demonstrate the wider applicability of the system. Digitized microscope images were analyzed with software that identified the filaments by comparing their dimensions with specified acceptance ranges and automatically measured selected parameters. Validation of the method against estimates obtained by conventional microscope measurements showed excellent agreement for both Aphanizomenon sp. and Trichodesmium sp. Compared with previously described image analysis methods based on fluorescence, the presented method is an improvement, as filament dimensions are used to discriminate between the cyanobacterial filaments and other objects. The image analysis also provides detailed morphological information on individual filaments, and the fully automated procedure requires only computer time for counting and is therefore highly cost‐efficient.
Habitat structure and fish: assessing the role of habitat complexity for fish using a small, semiportable, 3‐D underwater observatory
Authors: Fischer Philipp , Weber Arnd , Heine Georg , Weber Harald
Published: April 2011

In contrast to terrestrial ecology, three‐dimensional (3‐D) imaging technology is not well established as a method for studying species‐habitat interactions in aquatic ecology. In this study, we used a semi‐portable, digital, 3‐D underwater observatory designed for long‐term exposure in shallow water habitats to assess fish‐habitat interactions to artificial structures of different complexity. The observatory was mounted on a cable‐car system and was moved along a 50 m transect parallel to five artificial structures of different complexity and one control site. The optical unit took high‐resolution digital images, in pairs, from each structure and the control site at a frequency of 30 min over 24 h and was then moved remotely to the next structure. The system was operated for 2 mo without being recovered and took a total of 2160 stereoscopic image pairs. The system proved highly valuable in assessing small‐scale temporal patterns in fish‐habitat interactions, as well as changes in habitat preferences of fish over the diel cycle. Such small‐scale temporal and spatial patterns are important for a detailed understanding of specieshabitat interactions, not only in fish but also in most aquatic macro‐organisms. Nevertheless, such patterns can hardly be assessed using classical sampling devices due to labor and animal protection restrictions. However, the possibility of a significant increase in quantity of sampling through the use of remote imaging technology is accompanied by a significant increase in labor costs for image analysis. Therefore, further progress in semi‐ and fully automated systems for image analysis is needed, including 3‐D imaging tools, for ecological studies.
A novel radioactivity microsensor for high spatial resolution measurements of β radiation
Authors: Filthuth Heinz , Eickert Gabriele , Faerber Paul , Jonkers Henk M. , Polerecky Lubos , de Beer Dirk
Published: April 2011

We developed a microsensor for the detection of β‐radiation with submillimeter spatial resolution. The microsensor consists of a scintillating sphere (diameter 100‐300 µm) glued to a tip of an optical fiber (core diameter 140 µm) enclosed in a thin glass capillary. The scintillating sphere was made by embedding YLu scintillation powder and TiO2 light scattering particles in a methacrylate matrix. Photons generated in the scintillator by the β‐particles are guided through the fiber and detected by a photomultiplier connected to the opposite fiber end. The photon counts generated by the photomultiplier are linearly proportional to the volume‐specific radioactivity in the sample. The background signal can be suppressed practically to zero if two fibers connected to two photomultipliers working in coincidence are used. This, however, results in slightly diminished sensor performance (lower sensitivity and signal‐to‐noise ratio). As examples of applications, the diffusion coefficients of 36Cl‐, H14CO3−, and 45Ca2+ in agar‐solidified saline water were measured, and the depth distribution of primary productivity in an intact microbial mat was determined from vertical profiles of 14C after incubation in the light using H14CO3− as tracer.
Lipid extraction has little effect on the δ15N of aquatic consumers
Authors: Ingram Travis , Matthews Blake , Harrod Chris , Stephens Tom , Grey Jonathan , Markel Russell , Mazumder Asit
Published: April 2011

Proper application of stable isotopes (e.g., δ15N and δ13C) to food web analysis requires an understanding of all nondietary factors that contribute to isotopic variability. Lipid extraction is often used during stable isotope analysis (SIA), because synthesized lipids have a low δ13C and can mask the δ13C of a consumer's diet. Recent studies indicate that lipid extraction intended to adjust δ13C may also cause shifts in δ15N, but the magnitude of and reasons for the shift are highly uncertain. We examined a large data set (n = 854) for effects of lipid extraction (using Bligh and Dyer's [1959] chloroform‐methanol solvent mixtures) on the δ15N of aquatic consumers. We found no effect of chemically extracting lipids on the δ15N of whole zooplankton, unionid mussels, and fish liver samples, and found a small increase in fish muscle δ15N of ~0.4‰. We also detected a negative relationship between the shift in δ15N following extraction and the C:N ratio in muscle tissue, suggesting that effects of extraction were greater for tissue with lower lipid content. As long as appropriate techniques such as those from Bligh and Dyer (1959) are used, effects of lipid extraction on δ15N of aquatic consumers need not be a major consideration in the SIA of food webs.
Underwater infrared video system for behavioral studies in lakes
Authors: Chidami Saad , Guénard Guillaume , Amyot Marc
Published: April 2011

We propose the use of infrared (IR) video systems for the underwater behavioral study of animals at night, at depth, and/or in colored aquatic systems. This system is composed of a black‐and‐white video camera coupled with four projectors, each equipped with 50 IR light‐emitting diodes (LEDs). The use of LEDs is energetically far more efficient than the use of halogen lights equipped with IR filters, and therefore allows automatic long‐term video recording at low cost. Laboratory testing of one LED spot at increasing humic acid concentrations indicates that this system can be used for short‐range underwater observation in colored lakes. We applied this system to the study of scavenger/carcass interactions. Under field conditions, the setup is not easily detected by animals and allows direct and continuous observation of animal interactions during a full daily cycle. Note that, to our knowledge, this video system provides the first published night movies of freshwater fish behavior filmed in highly colored lakes, without using visible light. Our results indicate that this nonintrusive system can be successfully used for scientific studies in freshwater ecology, even in the presence of significant concentrations of light‐absorbing humic substances in the water.
Estimation of hyporheic water residence time in situ using 222Rn disequilibrium
Authors: Lamontagne Sébastien , Cook Peter G.
Published: April 2011

Radon‐222 is a naturally occurring radioactive gas (half‐life = 3.8 d) that is emitted by virtually all geologic materials. Stream sediment porewater tends to approach an equilibrium 222Rn activity determined by the 222Rn production rate of the sediments and radon half‐life. However, this equilibrium may not be reached when porewaters are diluted with low 222Rn surface waters by hyporheic exchange. Thus, the hyporheic water residence time (th) can be estimated in situ based on the difference in measured hyporheic 222Rn activity relative to 222Rn activity in the absence of hyporheic exchange. To validate 222Rn‐derived th estimates, a pulse in‐stream bromide injection and a continuous in‐stream injection of sulfur hexafluoride (SF6) were made in a subtropical stream (Swamp Oak Creek, Australia) along a reach with a sand, gravel, and cobble streambed. The bromide injection estimated th indirectly from the shape of upstream and downstream in‐stream breakthrough curves, whereas the SF6 injection estimated th directly by the determination of hyporheic breakthrough curves. The average th obtained with 222Rn disequilibrium (0.095 ± 0.086 d; ± SD) was similar to that obtained using bromide injection (0.10 ± 0.026 d) and within the range estimated from SF6 injection (0.05−0.2 d). Unlike the commonly used instream breakthough curves of injected tracers, the 222Rn disequilibrium technique is advantageous because it measures th of transient storage for the hyporheic zone only. The 222Rn disequilibrium technique is only applicable to estimate th in the range of hours to days, but this is the range of interest in many hyporheic studies.
A new method for quantitative analysis of helium isotopes in sediment pore‐waters
Authors: Chaduteau Carine , Fourré Elise , Jean‐Baptiste Philippe , Dapoigny Arnaud , Baumier Dominique , Charlou Jean‐Luc
Published: April 2011

Owing to their inertness and contrasted composition in the various earth reservoirs, helium isotopes are powerful tracers of a number of processes pertaining to geophysics and geochemistry. Because sediments cover a large portion of the earth's surface, helium isotope geochemistry of sediment pore‐waters is of particular interest. In spite of this potential, its development has been hampered by the difficulty of collecting samples without gas loss and/or contamination problems. We developed a new method for the sampling and the quantitative extraction of dissolved helium from sediment pore‐waters, leading to the determination of 3He and 4He concentration profiles. Core sampling is non‐destructive (no squeezing). The principle of the method is to use standard copper tubes (1.2 cm OD/25 cm in length), subsequently sealed with clamps, to take mini‐cores along the sediment core immediately following its retrieval. In the lab, the sediment is transferred from the copper tube to a noble gas extraction line by applying pressurized helium‐free water at one end of the copper tube. This technique allows dissolved helium to be recovered and analyzed using standard procedures for water samples. Tests were carried out successfully on an artificial core equilibrated with air to check the extraction efficiency in the same conditions as for real cores. The validity of the method was further confirmed by acquiring a vertical helium profile from a real marine core from the Zaire deep‐sea fan, illustrating some possible applications.
Ecological size‐frequency distributions: how to prevent and correct biases in spatial sampling
Authors: Zvuloni Assaf , Artzy‐Randrup Yael , Stone Lewi , van Woesik Robert , Loya Yossi
Published: April 2011

Size‐frequency distributions (SFDs) have been used to assess the ecological status of different populations in a variety of ecosystems and recently have become widely used to examine reef corals. SFDs may reflect the response of time‐varying influences of the environment, including the intensity and frequency of disturbances and the degree of environmental degradation. Here we elucidate the biases that can arise in the application of popular and traditional sampling methods (e.g. quadrat, belt‐transect, and line‐intercept). We show that these biases on the estimated SFD arise due to boundary effects of the sampling units. Incorrect evaluations of SFDs may lead to biased estimations of the ecological status of coral populations and may result in, among other things, erroneous nature reserve management policies. Our analysis is based on analytical calculations, simulations, and field observations. We have developed simple mathematical corrections, which provide unbiased estimations for previously collected data acquired by these widely used methods. In addition, we offer alternative sampling methods that do not suffer from these shortcomings. Eliminating these types of sampling errors will not only provide better assessments of the status of a given coral reef, but will also make way for more precise comparisons among coral reefs in different regions. Although we discuss the biases of SFDs in regard to reef coral populations, the work is equally relevant in other ecological contexts.
An “Integrated Sediment Disturber” (ISD) to study the impact of repeated physical perturbations on sediment geochemistry and the small benthic biota
Authors: Soltwedel Thomas , Lansard Bruno , Gilbert Franck , Hasemann Christiane , Bell Elanor , Sablotny Burkhard , Eagle Matthew , Kershaw Peter , Rabouille Christophe
Published: April 2011

An Integrated Sediment Disturber (ISD) was developed to study the effects of repeated physical disturbances on sediment geochemistry and associated benthic fauna. The ISD is capable to generate a strong, more or less uniform mixing of surface sediments by three rotating fork‐like disturber units of approximately 1 m in diameter. Perturbations can be set at different intensities and frequencies, e.g., on times scales of hours, days, or weeks, depending on the experimental design. The ISD carries an Autonomous Positioning Drive (APD) module, which allows the three‐dimensional positioning of sensors by a programmable controller. The three circular disturbed zones and an undisturbed control area in‐between can be monitored at specified frequencies using a microprofiler with microelectrodes for measuring various parameters (e.g., oxygen, pH, hydrogen sulphide). All operations are supervised by a digital stills camera. Sediment sampling at the start and end point using coring devices handled by divers (and potentially undertaken using a Remotely Operated Vehicle) provides material to study shifts in biodiversity of the small sedimentinhabiting biota and alterations in ecosystem functioning in response to perturbations and the changing geochemical characteristics of surface sediments.
Modeling zooplankton development using the monotonic upstream scheme for conservation laws
Authors: Record Nicholas R. , Pershing Andrew J.
Published: April 2011

Numerical diffusion along the age/stage axis is recognized as a significant problem in the modeling of zooplankton populations in dynamic physical environments. We demonstrate the utility of borrowing schemes from numerical fluid dynamics to address this problem. In particular, we use the monotonic upstream scheme for conservation laws (MUSCL) to model the zooplankton Calanus finmarchicus in the Gulf of Maine. Applying this scheme to the molting term substantially reduces numerical diffusion without requiring the introduction of additional state variables. The improvement is on average equivalent to a 3‐ to 5‐fold increase in the number of state variables, but without the run‐time costs of such an increase. Basic strategies for assessing numerical schemes are discussed, and some consequences of numerical diffusion in the age domain are demonstrated.
In situ measurement of gross photosynthesis using a microsensor‐based light‐shade shift method
Authors: Polerecky Lubos , Lott Christian , Weber Miriam
Published: April 2011

We present a measuring procedure that allows the quantification of gross photosynthesis at the ambient light intensity, P(I), from light transition measurements similar to those employed in the light‐dark shift method but without the necessity of achieving complete darkness. The method is thus more readily applicable in situ, where, during daylight, complete sample darkening is very difficult or even impossible to achieve. The procedure involves rapid microsensor‐based monitoring of oxygen in the sample during a series of light transitions from ambient light intensity to a few intermediate levels, and determination of the initial rates of oxygen decrease during each partial darkening (shading) period. P(I) is then recovered by fitting the measured rates with a function derived from the model describing the change in photosynthesis rate with light intensity (P‐I curve) and extrapolating it to the full light‐to‐dark transition. We validated this approach in the lab on coral and microbial mat samples and found that a satisfactory estimate of P(I) can be obtained with as few as 4–5 shade levels. We also applied the procedure in situ and showed that the gross photosynthesis rate at the ambient sunlight in the microbial mat and in the coral reached, respectively, approximately 50% to 65% and 94% to 97% of the saturated rate.
A commercially available rosette system for trace metal—clean sampling
Authors: Measures Christopher I. , Landing William M. , Brown Matthew T. , Buck Clifton S.
Published: April 2011

To obtain trace element data sets of sufficient resolution to resolve and interpret biogeochemical features, it is necessary to develop sampling schemes that are fast and reliable, retrieve uncontaminated samples, and are consistent with the new global‐ranging oceanographic programs. We present here a detailed description of a rosette‐based system for trace element determinations that meets these criteria. It has been used successfully on several CLIVAR cruises that required high‐resolution sampling for trace elements, and it has also been used on cruises for biological studies where large volumes of uncontaminated water were needed for deckboard incubations. With the exception of the weights used for ballasting, the rosette is an assembly of commercially available components and thus requires no custom fabrication. Comparison of Fe and other trace element concentrations in samples collected with this equipment and processed using these protocols with samples collected and processed using protocols developed in other trace element laboratories, during the SAFe intercalibration cruise, show essentially identical results.
Evaluation of metabolism models for free‐water dissolved oxygen methods in lakes
Authors: Hanson Paul C. , Carpenter Stephen R. , Kimura Nobuaki , Wu Chin , Cornelius Sean P. , Kratz Timothy K.
Published: April 2011

Free‐water measurements of dissolved oxygen (DO) in lakes are becoming common and provide opportunities for estimating ecosystem processes, such as gross primary production (GPP) and ecosystem respiration (R). The models used to estimate metabolism often subsume biological processes into one parameter each for GPP and R. However, high‐frequency DO observations made over days show diverse patterns at multiple time scales, suggesting a complex suite of processes controls DO dynamics. Can we improve metabolism estimates and predictive ability for DO at diel scales by adding complexity to the models? In this study, we use data from two north temperate lakes to test a variety of metabolism models representing a suite of non‐linear metabolic processes. To test whether alternative models can be discriminated, we simulated DO with assumed parameter values and auto‐regressive noise, and fit the models to the simulated DO. The most complex model could be discriminated from simpler models and provided the most accurate and precise predictions. However, when models were fit to observed DO data from the sensor network, the simplest model predicted DO as well as the most complex one. The added complexity did not improve model performance. An analysis of the model residuals indicates that physics may explain some of the DO pattern not predicted, especially high‐frequency oscillations and anomalies that appear to coincide with weather patterns. Under reasonably stable weather conditions and at scales of a few days, simple metabolism models explain the bulk of diel DO variability.
A critical assessment of different transmethylation procedures commonly employed in the fatty acid analysis of aquatic organisms
Authors: Schlechtriem Christian , Henderson R. James , Tocher Douglas R.
Published: April 2011

Several transmethylation procedures have been used for fatty acid analysis of aquatic organisms, although the suitability of the applied procedures has rarely been tested. The aim of this study was to demonstrate how different derivatization procedures can affect the result of fatty acid analysis. Different transmethylation procedures based on the acidic catalysts boron trifluoride, concentrated sulphuric acid, and anhydrous hydrochloric acid were applied to cold‐pressed copepod oil and Atlantic salmon flesh lipids rich in wax esters and triacylglycerols, respectively. The results show that (1) the use of unsuitable catalysts and/or incubation conditions may influence the data obtained, which can lead to inaccurate conclusions about the presence of fatty acids in aquatic organisms/ecosystems, (2) different derivatization procedures based on the same catalyst can produce diverging results, and (3) the efficiency of a selected catalyst/procedure should be verified (e.g., by thin‐layer chromatography) to ensure the complete transmethylation of fatty acids.
Entry approach into pristine ice‐sealed lakes—Lake Vida, East Antarctica, a model ecosystem
Authors: Doran Peter T. , Fritsen Christian H. , Murray Alison E. , Kenig Fabien , McKay Chris P. , Kyne Jay D.
Published: April 2011

Ice‐sealed lakes, potentially home to novel microbiota and microbial processes, can provide a window into isolated and geologically ancient systems. These habitats are earth analogs for extraterrestrial systems that have yet to be sampled, though potentially harbor, or have harbored life at some time during their past. They are also small‐scale models of the numerous sub‐glacial lake systems, which have been identified across Antarctica and in Iceland. Methods are needed to sample these ecosystems with environmental stewardship in mind, in which human impact on the ecosystem is mitigated before and during sampling. This report describes an entry and sampling approach that was executed at Lake Vida, East Antarctica, a permanently ice‐sealed lake that has never been sampled. Best practice sampling procedures were developed with emphasis on mitigating introduction of trace organics or microbiota to the ecosystem. The conceptual approach is transferable to other isolated pristine aquatic ecosystems on Earth and elsewhere.
Estimation of regional richness in marine benthic communities: quantifying the error
Authors: Canning‐Clode João , Valdivia Nelson , Molis Markus , Thomason Jeremy C. , Wahl Martin
Published: April 2011

Species richness is the most widely used measure of biodiversity. It is considered crucial for testing numerous ecological theories. While local species richness is easily determined by sampling, the quantification of regional richness relies on more or less complete species inventories, expert estimation, or mathematical extrapolation from a number of replicated local samplings. However the accuracy of such extrapolations is rarely known. In this study, we compare the common estimators MM (Michaelis‐Menten), Chao1, Chao2, ACE (Abundance‐based Coverage Estimator), and the first and second order Jackknifes against the asymptote of the species accumulation curve, which we use as an estimate of true regional richness. Subsequently, we quantified the role of sample size, i.e., number of replicates, for precision, accuracy, and bias of the estimation. These replicates were sub‐sets of three large data sets of benthic assemblages from the NE Atlantic: (i) soft‐bottom sediment communities in the Western Baltic (n = 70); (ii) hard‐bottom communities from emergent rock on the Island of Helgoland, North Sea (n = 52), and (iii) hard‐bottom assemblages grown on artificial substrata in Madeira Island, Portugal (n = 56). For all community types, Jack2 showed a better performance in terms of bias and accuracy while MM exhibited the highest precision. However, in virtually all cases and across all sampling efforts, the estimators underestimated the regional species richness, regardless of habitat type, or selected estimator. Generally, the amount of underestimation decreased with sampling effort. A logarithmic function was applied to quantify the bias caused by low replication using the best estimator, Jack2. The bias was more obvious in the soft‐bottom environment, followed by the natural hard‐bottom and the artificial hard‐bottom habitats, respectively. If a weaker estimator in terms of performance is chosen for this quantification, more replicates are required to obtain a reliable estimation of regional richness.
MAGIC method for subnanomolar orthophosphate determination in freshwater
Authors: Anagnostou Eleni , Sherrell Robert M.
Published: April 2011

A freshwater magnesium hydroxide coprecipitation method (MAGIC) has been developed to accurately and reproducibly determine low (nanomolar to subnanomolar) soluble reactive phosphorus (SRP) concentrations in freshwater. The method allows investigation of phosphorus distributions and cycling for systems in which SRP is below the detection limits of conventional methods. In natural waters, both inorganic and organic forms of P are coprecipitated; hence the method is essentially a preconcentration rather than a separation technique. Quantification of SRP on dissolved MAGIC precipitates follows a modified version of the standard molybdenum blue colorimetric method, using a spectrophotometer with ~0.1 milliabsorbance (mAbs) noise. Detection limit is 0.15 nM, improving on typical conventional colorimetric methods by a factor of ~50, with precision (RSD of triplicates) of ~10% at the 1 nM SRP level, 10% at ≤0.5 nM, and 4% to 7% at >1 nM. Considerable method development was necessary to eliminate or correct for multiple interferences, including a novel finding of potential interference by colored dissolved organic matter, and to optimize recovery, precision, and detection limit. The method was applied to filtered, frozen samples from western Lake Superior, showing that SRP concentrations are characterized by limited seasonal variability, largely uniform vertical distribution, and near‐bottom enrichment. Concentrations ranged from 0.4 to 10.9 nM SRP, representing ~10% of the total dissolved phosphorus pool. MAGIC is an easily employed analytical method appropriate for measurement of very low SRP in lakes and rivers.
Automated processing of coral reef benthic images
Authors: Stokes M. Dale , Deane Grant B.
Published: April 2011

We describe an automated computer algorithm for the classification of coral reef benthic organisms and substrates sampled using a typical photographic quadrat survey. The technique compares subsections of a quadrat sample image (blocks) to a library of identified species blocks and computes a distance or probability of identification in a multidimensional hypervolume of discrimination metrics. The discrimination metrics include texture (calculated from a radial sampling of a two‐dimensional discrete cosine transform) and three channels of a normalized color space. A standard multivariate classification technique based on the Mahalanobis distance was unsuccessful in discriminating substrata because of the large morphological variation inherent in reef organisms. An alternative classification scheme based on an exhaustive search through an organism reference library yielded classification maps comparable to those obtained by manual analysis.
Comparison of measurement methods for radium‐226 on manganese‐fiber
Authors: Peterson Richard N. , Burnett William C. , Dimova Natasha , Santos Isaac R.
Published: April 2011

Acrylic fibers impregnated with MnO2 (Mn‐fiber) have become a valuable tool for concentrating dissolved radium for oceanographic applications. With four naturally‐occurring radium isotopes (223Ra, 224Ra, 226Ra, and 228Ra) of vastly different half‐lives (3.6 days to 1600 years), radium can be a powerful tool for tracing terrestrial water discharges into the ocean and studying coastal mixing processes. Several techniques have been outlined in the literature describing the measurement of 226Ra on Mn‐fiber via its gaseous daughter, 222Rn. We present a proven, air‐tight cartridge design that allows one to use these measurement techniques. We then review the procedures for three radon‐based nondestructive measurement techniques for 226Ra on Mn‐fiber (via RAD7, RaDeCC, and Rn emanation line systems) and perform an intercomparison among them, using the standard technique of γ‐spectrometry as a reference. We find that all methods statistically agree in terms of measured activity. The Rn emanation line and the RaDeCC systems (both based on Lucas cell counting) provide the lowest measurement uncertainties and minimum detectable activities (MDAs) for a given counting time. The RAD7 technique, on the other hand, offers the advantage of being an automated system, thus requiring minimal user interaction. The standard γ‐spectrometry technique, while more time‐consuming and sample destructive, has the advantage of providing a simultaneous measurement for 228Ra.
Determination of iron(II) in acidified seawater samples by luminol chemiluminescence
Authors: Hansard S. Paul , Landing William M.
Published: April 2011

The redox speciation of iron has been proposed to influence the biological uptake of iron, yet little is known of its true redox partitioning in the open ocean. This is due to its extremely low concentration and to the tendency for the reduced species, Fe(II), to undergo rapid oxidation before analyses can be undertaken. Although several methods have been developed to measure Fe(II), many require extensive sample preparation and delicate instrumentation which limit their utility in the field. Also, because most lack sufficient sensitivity to make direct measurements, a preconcentration step is often required, introducing the potential for significant artifacts. For these reasons, the existing open ocean Fe(II) dataset has been both limited in scope and internally inconsistent. We recently used a highly sensitive chemiluminescent method to measure Fe(II) in 1452 samples collected at 121 stations in the Pacific Ocean. The method allowed for rapid analyses to be made with minimal sample preparation and no preconcentration. To overcome the logistical problems arising from rapid oxidation of Fe(II), we modified this method to include a modest pH adjustment of the sample, which greatly increases the half‐life of Fe(II). Herein, details of the method are presented and analytical performance is assessed under actual field conditions. Potential interferences are evaluated and minor artifacts arising from sample acidification are discussed.
Creation of a pilot metatranscriptome library from eukaryotic plankton of a eutrophic bay (Tampa Bay, Florida)
Authors: John David E. , Zielinski Brian L. , Paul John H.
Published: April 2011

Analysis of the suite of genes expressed by natural populations of phytoplankton can potentially elucidate valuable information about the types, cellular activity, and biogeochemical impacts of organisms present in the marine environment. Here we describe the construction of a pilot metatranscriptome library created from eukaryotic planktonic organisms in Tampa Bay, FL, USA. RNA from cells greater than 2 µm was extracted and purified, and poly(A) tailed mRNA was concentrated and amplified using linear amplification chemistry. Amplified RNA was converted to double‐stranded cDNA using reverse transcriptase and DNA polymerase I (Klenow fragment) and cloned, and 232 clones were sequenced. Sequences with significant GenBank BLAST homology revealed genes related to photosynthesis and nutrient acquisition, along with general cell functions. In total, 27% of sequenced transcript clones contained significant homology to GenBank sequences, 2% of the total were putatively derived from ribosomal RNA, and 1% were most similar to sequences originating from prokaryotes. About 70% of the identified transcripts were putatively derived from eukaryotic phytoplankton, including diatoms, chlorophytes, and dinoflagellates. Although small in scale, this study provides the basis for future efforts to characterize the metatranscriptome of marine phytoplankton populations.
Expressing biomarker data in stoichiometric terms: shifts in distribution and biogeochemical interpretation
Authors: Panetta Robert J. , Gélinas Yves
Published: April 2011

Quantitative biomarker analysis is an invaluable tool used routinely by organic geochemists to interpret and explain environmental processes. Since the advent of organic geochemistry, all levels of biomarker methodology from wet chemistry to data interpretation have significantly advanced; however, an important aspect of data analysis has remained constant and that is the expression of biomarkers in terms of mass (e.g., mg gOC−1). We argue that biomarkers are more appropriately expressed in terms of moles (e.g., mmol molOC−1) to better reflect molecular‐level distribution of compounds of interest, as well as introducing a chemical consistency for better comparability and transferability between data sets. Using modeled and real data culled from the literature, we demonstrate that the use of moles is not a trivial conversion and that distribution and relative weighting of biomarker data sets are shifted and affect the total data structure. The shift is sometimes strong enough to exert changes in interpretation (e.g., microbial abundance in an estuarine system), alter proxies (e.g., terrestrial‐to‐aquatic ratio), and potentially influence the use of multivariate statistical methods (e.g., principal components analysis).
Copepod feeding quantified by planar laser imaging of gut fluorescence
Authors: Karaköylü Erdem M. , Franks Peter J. S. , Tanaka Yuji , Roberts Paul L. D. , Jaffe Jules S.
Published: April 2011

We present a new method for quantifying the feeding of individual copepods, using a planar sheet of laser light to stimulate the fluorescence of phytoplankton ingested by the copepod. The fluorescence is imaged with a sensitive CCD camera, giving two‐dimensional images of the copepod's gut with 20 × 20 µm spatial resolution. Using tethered copepods, we have obtained > 3 h long time series of copepod gut fluorescence with images every 15–20 s. The same individual copepod can be used for multiple experiments, obviating the problems of individual variability as a source of error. Initial data reveal two distinct patterns of variability as material moves through two functionally different gut compartments. These patterns reflect processes occurring in each compartment. The upper (anterior) mid‐gut shows higher variability and less repeatability than the posterior midgut where undigested material is aggregated into a fecal pellet and evacuated at regular intervals. Variability in the upper mid‐gut is likely due to factors such as intermittence of feeding and relatively complex mixing dynamics. In the posterior mid‐gut, mixing dynamics are much simpler, and the variability of the upper compartment is integrated over the time scale of pellet formation.
Desalination plants as plankton sampling devices in temporal studies: proof‐of‐concept and suggestions for the future
Authors: Sewell Mary A. , Jury Jennifer A.
Published: April 2011

Long‐term records of zooplankton distribution and abundance are increasingly being used as indicators of climate change. The North Atlantic, because of the 80 years of Continuous Plankton Recorder (CPR) surveys, is well‐represented with such time series. However, there are few long‐term data sets from the Pacific Ocean and especially from Antarctica, where traditional plankton sampling is logistically challenging. Here we test an alternative sampling method, the primary filter (PF) of the Scott Base reverse‐osmosis (RO) desalination plant, which had the same mesh size (100 µm) as our standard plankton tows. We show, by qualitative comparison to fresh plankton samples collected with a plankton net, that the PF collects a representative zooplankton community, does not damage delicate or fragile forms (e.g., appendicularians, ctenophores, medusae, chaetognaths, pteropods, polychaetes, embryos with intact fertilization membranes, pilidia, bipinnaria), and that the large volumes of seawater filtered allow collection of rare meroplankton members. We further show that seasonal changes can be detected in the zooplankton when PF samples are fixed in formalin for later analysis. Desalination plant PFs may provide an innovative solution to study temporal patterns in the Antarctic zooplankton and have the potential to provide long‐term data sets from other poorly sampled regions.
Effect of acid Lugol solution as preservative on two representative chitineous and gelatinous zooplankton groups
Authors: Jaspers Cornelia , Carstensen Jacob
Published: April 2011

The estimation of biomass from body lengths to carbon regressions is a common approach in plankton research. Several different chemicals for sample preservation are in use, and conversion factors to account for shrinkage effects exist, but to our knowledge the consequences of using potassium‐iodide and iodine (Lugol solution) as preservative on body sizes of different mesozooplankton groups have not been investigated. We tested the effect of 2% acidified Lugol solution on body sizes over time on two major marine mesozooplankton groups, namely larvaceans and copepods, which are representatives of gelatinous and chitineous plankton, respectively. For both, we observed a significant shrinkage effect over time (P < 0.0001). Larvaceans showed a reduction in body size by 20% within the first 2 min, which stabilized after 36 h at 22%, whereas copepods shrank by 17%. These differences were significant (P = 0.0324), with no further shrinkage observed over an additional 3 months. Failure to adequately account for shrinkage effects could result in significant biomass under‐estimation if length‐weight relationships are generated from live material.
Improved cyanolysis protocol for detection of zero‐valent sulfur in natural aquatic systems
Authors: Kamyshny Alexey
Published: April 2011

We propose a novel protocol for detection of reactive zero‐valent sulfur (ZVS) in natural aquatic samples including seawater. Reaction with hot potassium cyanide at slightly acidic conditions recovers ZVS from colloidal fraction of particulate elemental sulfur, polysulfides (Sn2−), and their protonated forms. Preconcentration by partial evaporation of the sample and separation of thiocyanate anions by high‐performance liquid chromatography on the C30 reverse phase column modified with poly(ethylene glycol) followed by spectrophotometric detection at 220 nm wavelength allows us to detect reactive ZVS with detection limit of 3 nmol L−1 for fresh water samples and 6 nmol L−1 for seawater samples. Storage at 4°C for 6 weeks does not change the concentration of thiocyanate in the sample by more than 10%.
Discriminating between intra‐ and extracellular metals using chemical extractions: an update on the case of iron
Authors: Hassler Christel S. , Schoemann Véronique
Published: April 2011

Iron influences the climate system by limiting primary productivity. It is therefore essential to accurately measure the iron fraction associated with phytoplankton in aquatic systems. A washing procedure using EDTA, being efficient for numerous trace metals, is not strong enough to remove iron adsorbed to the surface of microorganisms. Stronger washing solutions are used for iron, but these have only been assessed for a marine diatom. This study assesses the applicability of the oxalate washing procedure for both fresh‐ and seawater aquatic systems. We assessed iron solubilization as a result of oxalate washing in both synthetic and natural freshwater and seawater, and we tested it on several model phytoplankton and natural assemblages from Lake Champlain, the Southern Ocean, and the Derwent River estuary. We report the effects of the oxalate solution contact time, concentration, and amendment. Our study shows that 20‐min washing provides an efficient measurement of the intracellular phytoplanktonic pool of iron in both freshwater and seawater. The direct amendment of oxalate in the experimental solution presents many advantages that are critical for the measurement of size‐fractionated particulate iron. These include fine control of bioaccumulation termination, a significant gain in time, and homogeneity of the washing treatment.
Surface adhesion measurements in aquatic biofilms using magnetic particle induction: MagPI
Authors: Larson Fredrik , Lubarsky Helen , Gerbersdorf Sabine U. , Paterson David M.
Published: April 2011

Natural sediment stability is a product of interacting physical and biological factors, and whereas stability can be measured, few techniques allow sensitive assessment of the sediment surface as conditions change. For example, stability gradually increases as a biofilm develops or as salinity rises, or it might be influenced by toxic compounds. This article introduces a new technique (magnetic particle induction: MagPI) based on the magnetic attraction of specially produced fluorescent ferrous particles. The test particles are added to a surface and subjected to an incrementally increasing magnetic field produced by permanent magnets or electromagnets. There is a strong correlation between magnetic flux density (mTesla) and distance from the surface (r2 = 0.99) for permanent magnets and between magnetic flux density and the current supplied to an electromagnet (r2 > 0.95). The magnetic force at which the particles are recaptured is determined as a measure of surface adhesion. MagPI therefore determines the “stickiness” of the surface, whether a biofilm, sediment, or other material. The average magnetic flux density required to remove test particles from diatom biofilms (15.5 mTesla) was significantly greater than from cyanobacterial biofilms (10 mTesla). Controls of fine glass beads showed little adhesion (2.2 mTesla). Surface adhesion is an important bed property reflecting the sediment system's potential to capture and retain new particles and accumulate material. MagPI offers a straightforward and economic way to determine the surface adhesion of a variety of surfaces rapidly and with precision. The technique may have applications in physical, environmental, and biomedical research.
Simple staining method for differentiating live and dead marine zooplankton in field samples
Authors: Elliott David T. , Tang Kam W.
Published: April 2011

We describe and evaluate a method for the use of neutral red staining to differentiate live and dead zooplankton in marine field samples. The protocol can be easily incorporated into shipboard zooplankton sampling. The use of neutral red in laboratory studies is common, but its application for quantifying natural live/dead zooplankton composition under field conditions has not been evaluated in detail. We tested the accuracy and precision of the method for a range of salinities and temperatures, and for common estuarine zooplankton groups. Detailed descriptions of staining intensities and patterns are provided. In addition, we evaluated potential artifact mortality due to collection and sample handling. The method produced accurate results under conditions tested, and artifact mortality was negligible using the recommended protocol. Neutral red staining is ideal for quantification of zooplankton carcasses in field samples, which will allow for more systematic study of in situ zooplankton mortality and related processes.
New approach for measuring denitrification in the rhizosphere of vegetated marsh sediments
Authors: Koop‐Jakobsen Ketil , Giblin Anne E.
Published: April 2011

This study presents a new approach for measuring denitrification at depth in the marsh rhizosphere (below 5 cm). The method combines the push‐pull technique and the 15N‐isotope pairing technique, here referred to as the PPIPT. The PPIPT allows ambient denitrification rates to be measured in situ at depth in the marsh rhizosphere with minimal damage to roots and rhizomes and minimal disturbance of the ambient pore water composition. In this method, pore water is extracted from the sediment using micropiezometers without contact with the atmosphere. The porewater is amended with 15NO3− to trace denitrification, and Ar(g) is added to trace potential gas loss of denitrification end products. The “spiked” pore water is injected back into the sediment for incubation. Subsequently, samples are sequentially extracted from the sediment for analysis of 28N2, 29N2, 30N2, and Ar. Denitrification rates are calculated using the isotope paring technique and corrected for dilution and gaseous losses using the argon tracer. After several trials in the laboratory and in the field to optimize the method, the PPIPT was applied in the field to measure denitrification in the rhizosphere of various vegetation zones in two New England marshes in northeastern USA. The field applications verified the PPIPT method as a useful tool for measuring ambient rates of denitrification at depth in salt marsh rhizospheres. Generally, the rates measured were low (0–12 µmol m−2 h−1) and showed a high spatial variability in the marsh rhizosphere among different vegetation zones.
Measuring atmospheric nutrient deposition to inland waters: Evaluation of direct methods
Authors: Blake Timothy W. , Downing John A.
Published: April 2011

Several methodological problems have been noted in analyses of atmospheric phosphorus (P) and nitrogen (N) deposition to inland waters. These include the quantification of contamination, rates of dry deposition of nutrients on wet and dry surfaces, and short‐range dust contamination. On and around a small lake in an agricultural region, we tested bulk and automated dry‐ and wet‐deposition samplers for the presence of insect and dust contamination and presented procedures to eliminate biases. Local (≤100 m) dust deposition appeared negligible, so land‐based measurements could be extrapolated to water; however, on‐ and near‐shore samplers collected more insect contaminants than off‐shore samplers. Insect contamination was large and most significant for estimates of P deposition, but a method to correct for it is proposed. We found that bulk and automated dryand wet‐deposition samplers yielded similar values when contamination was eliminated. Screens for atmospheric deposition samplers were tested and led to lowered insect contamination and similar deposition rates to samplers without them. Bulk sampling can provide acceptable estimates of atmospheric nutrient deposition if contamination is quantified or excluded. A wet surface does not differ significantly from a dry surface for measurement of dry‐fall of P. Short‐range transport of dust‐borne nutrients may be insignificant. Low‐cost bulk samplers yielded accurate measurements of atmospheric nutrient deposition.