Showing papers in "Limnology and Oceanography-methods in 2010"

Effect of instrument‐specific response on the analysis of fulvic acid fluorescence spectra

Abstract: Fluorescence spectroscopy has been extensively employed to characterize the source, age, and reactivity of aquatic dissolved organic matter (DOM). However, there is no consensus on the protocols for collecting and correcting DOM fluorescence spectra for the instrument-specific response associated with each component on a fluorometer involved in the excitation of DOM and the resulting detection of DOM emission. The central objective of this study was to evaluate the removal of instrument-specific response from DOM fluorescence spectra collected on three different fluorometers using manufacturer-provided emission and excitation correction files. We evaluated criteria and protocols for comparison of removal of instrument response, using quinine sulfate, a well-characterized fluorophore, as well as the International Humic Substance Society's microbially and terrestrially derived reference end-member fulvic acids: Pony Lake and Suwannee River fulvic acids, respectively. Our results demonstrate that sample spectra collected on different fluorometers differed significantly before correction. Although the effectiveness of manufacturer-provided correction factors in removal of instrument response from sample spectra varied by instrument, spectral overlap of the same sample on multiple instruments improved after correction. Our results suggest that conclusions based on analysis of trends within a dataset of DOM fluorescence spectra should be expected to be independent of the fluorometer employed.

Lake metabolism and the diel oxygen technique: State of the science

Abstract: Significant improvements have been made in estimating gross primary production (GPP), ecosystem respiration (R), and net ecosystem production (NEP) from diel, “free-water” changes in dissolved oxygen (DO). Here we evaluate some of the assumptions and uncertainties that are still embedded in the technique and provide guidelines on how to estimate reliable metabolic rates from high-frequency sonde data. True whole-system estimates are often not obtained because measurements reflect an unknown zone of influence which varies over space and time. A minimum logging frequency of 30 min was sufficient to capture metabolism at the daily time scale. Higher sampling frequencies capture additional pattern in the DO data, primarily related to physical mixing. Causes behind the often large daily variability are discussed and evaluated for an oligotrophic and a eutrophic lake. Despite a 3-fold higher day-to-day variability in absolute GPP rates in the eutrophic lake, both lakes required at least 3 sonde days per week for GPP estimates to be within 20% of the weekly average. A sensitivity analysis evaluated uncertainties associated with DO measurements, piston velocity (k), and the assumption that daytime R equals nighttime R. In low productivity lakes, uncertainty in DO measurements and piston velocity strongly impacts R but has no effect on GPP or NEP. Lack of accounting for higher R during the day underestimates R and GPP but has no effect on NEP. We finally provide suggestions for future research to improve the technique.

The Underwater Vision Profiler 5: An advanced instrument for high spatial resolution studies of particle size spectra and zooplankton

Abstract: The Underwater Vision Profiler (UVP) was developed to quantify the vertical distribution of macroscopic particles and zooplankton 100 mu m in size. The smaller size limit is fixed by optical resolution, whereas the larger size limit is determined by the volume of water illuminated per image. The new fifth generation instrument (UVP5) is compact (30 kg in air) and operates either as a stand-alone instrument with an independent power supply for use on a mooring or free-drifting array, or as a component of a Conductivity, Temperature, and Depth (CTD)-rosette package. Images are recorded at a frequency up to 6 Hz. If the UVP5 is interfaced with a CTD, these images are acquired and analyzed in real time. Images are recorded every 20 cm at the 1 m s(-1) lowering speed. The current maximum deployment depth is 3000 m. The recorded volume per image is 1.02 L, and the conversion equation from pixel area to size in mm(2) is S(m) = 0.003S(p)(1.3348) where S(p) is the surface of the particle in pixels and S(m) the surface in mm(2). Comparisons between the earlier UVP versions and UVP5 indicate that images ranging in size from 105 mu m to 2.66 mm are identical so historical and contemporary data sets can be compared.

Testing the Honeywell Durafet® for seawater pH applications

Abstract: We report on the first seawater tests at 1 atm of the Honeywell Durafet® pH sensor, a commercially available ion sensitive field effect transistor (ISFET). Performance of this sensor was evaluated in a number of different situations including a temperature-controlled calibration vessel, the MBARI test tank, shipboard underway mapping, and a surface mooring. Many of these tests included a secondary reference electrode in addition to the internal reference supplied with the stock Durafet sensor. We present a theoretical overview of sensor response using both types of reference electrode. The Durafet sensor operates with a short term precision of ± 0.0005 pH over periods of several hours and exhibits stability of better than 0.005 pH over periods of weeks to months. Our tests indicate that the Durafet pH sensor operates at a level of performance satisfactory for many types of biogeochemical studies at low pressure.

Multiple approaches to estimating air‐water gas exchange in small lakes

Abstract: The rate of gas exchange between air and water is an essential quantity in a number of contexts, from mass balances to the calculation of whole-system metabolism. The exchange of a gas between water and the atmosphere is controlled by differential partial pressures of gases in air and in water (both straightforward to measure) and by the amount of turbulent energy exchange between the air-water interface, the measurement of which is neither simple nor direct. This physical exchange is often expressed as a piston velocity (k). We compared four methods for estimating k in a series of small (0.3 to 45 ha), low-wind (mean wind < 3 m s–1) lakes: 1) floating chambers using ambient CH4; 2) whole-lake SF6 additions; 3) three wind-based models from the literature; and 4) C mass balances constrained by whole-lake 13C additions. All of the methods, with the exception of one windbased model, converged on values for k600 of between 0.35 and 0.74 m d–1 with no biases among methods. The floating chambers, if designed properly, are a cost-effective way of obtaining site-specific values of k for low wind lakes over fairly short time frames (hours).

The application of holography to the analysis of size and settling velocity of suspended cohesive sediments

Abstract: Suspended cohesive sediments commonly occur in flocculated form. The flocculation process significantly increases particle size, settling velocity, and settling flux in comparison to unflocculated particles. To better understand suspended particles, a new instrument for in situ imaging using digital inline holography is presented and evaluated. With a resolution of 7.4 µm per pixel and a field of view of 7.4 × 7.4 mm, the instrument generates sharply focused images of particles from approximately 20 µm to 7 mm in diameter at up to 25 frames per second. A significant advantage of holography over current imaging systems is that in-focus images are obtained over a substantial depth of field. Contained in small-diameter cylindrical housings, the instrument presents minimal flow disruption and is easily deployable. Digitally recorded holograms are reconstructed and analyzed for number and size of particles in a fully automated manner. To assess the systems' potential, particle size distributions for two grades of quartz sand are compared with those from a laser diffraction particle sizer and are found to exhibit good similarity. To simultaneously estimate particle size and settling velocity, a modification to the system is demonstrated in which settling particles are automatically tracked and sized. The resulting relationships between settling velocity and effective density as functions of particle size are characteristic of suspended cohesive sediments and empirical power-law descriptors of these relationships show excellent agreement with previously published studies.

Tracer Additions for Spiraling Curve Characterization (TASCC): Quantifying stream nutrient uptake kinetics from ambient to saturation

Abstract: Stream nutrient tracer additions and nutrient spiraling metrics are frequently used to quantify lotic ecosystem behavior. Of particular concern is the influence nutrient concentration exerts on nutrient retention and export. However, characterizing spiraling response curves across a range of concentrations has remained challenging, in part due to the large effort required to develop these curves using traditional (e.g., plateau or steadystate) approaches. Here we outline and demonstrate a new approach to quantify nutrient uptake kinetics from ambient to saturation using Tracer Additions for Spiraling Curve Characterization (TASCC). This approach provides a rapid and relatively easy technique for quantifying ambient-spiraling parameters, nutrient uptake kinetics and kinetic model parameterization, and assessment of stream proximity to saturation. We compare the results from TASCC to traditional breakthrough curve integrated and plateau approaches. We highlight the advantages of the TASCC approach for characterizing continuous spiraling response curves from ambient to saturation with a single tracer addition experiment, and its applicability to larger rivers where achieving plateau conditions (i.e., steady-state) is impractical.

Estimating methane emissions from northern lakes using ice‐bubble surveys

Abstract: The magnitude and variability in methane (CH4) emissions from lakes are uncertain due to limitations in methods for quantifying the patchiness of ebullition (bubbling). We present a field method to estimate an important and highly uncertain source: ebullition from northern lakes. We defined four classes of CH4 bubble clusters trapped in lake ice representing distinct types of biogenic ebullition seeps that differed in flux rate. Mean annual ebullition determined through long-term (up to 700 d) continuous flux measurements of 31 seeps in three Siberian and one Alaskan lake was (mean ± standard error, 4–10 seeps per class; g CH4 seep−1 y−1): A, 6 ± 4; B, 48 ± 11; C, 354 ± 52; Hotspot, 1167 ± 177. Discrete-seep ebullition comprised up to 87% of total emissions from Siberian lakes when diffusive flux and background and seep ebullition were considered together. Including seep ebullition increased previous estimates of lake CH4 emissions based on traditional methods 5- to 8-fold for Siberian and Alaskan lakes. Linking new ebullition estimates to an established biogeochemical model, the Terrestrial Ecosystem Model, increased previous estimates of regional terrestrial CH4 emissions 3- to 7-fold in Siberia. Assessment of the method revealed that ebullition seeps are an important component of the terrestrial CH4 budget. They are identifiable by seep type by independent observers; they are consistent predictors of flux rate in both Siberia and Alaska; and they allow quantification of what was previously a large source of uncertainty in upscaling CH4 emissions from lakes to regions.

Using laser diffraction data to obtain accurate particle size distributions: the role of particle composition

Abstract: Suspended particle composition has a large influence on light scattering by small ( 250 µm) produced little effect; however, particles smaller than the lower limit (<1.25 µm) influenced concentrations over the entire LISST size range and produced counterintuitive effects, such as increased concentrations in the largest size bins.

A laboratory-based, experimental system for the study of ocean acidification effects on marine invertebrate larvae

Abstract: Ocean acidification, a reduction in ocean pH due to the uptake of anthropogenic carbon dioxide (CO2) by surface waters, has recently emerged as a research theme in marine biology due to an expected deleterious effect of altered seawater chemistry on calcification Owing to the importance of larval survival and dispersal for the maintenance of adult populations, early life history stages of calcifying marine invertebrates have been a central focus of this research Here, we present an experimental system that unites the culturing needs of larval invertebrates with methods for careful control, monitoring, and manipulation of seawater carbonate chemistry necessary to conduct laboratory-based studies of ocean acidification Using a series of mass flow controllers, the system produces three unique pCO2 levels, which are bubbled into gas-mixing reservoirs for equilibration with filtered seawater This seawater is then delivered to larval culturing vessels providing the larvae with a continual supply of clean seawater consistent with optimal culturing methodologies In this flow-through system, pCO2 levels are determined at 3 points: the inflowing seawater, the gas-mixing reservoirs, and the larval culture vessels The delivered gas pCO2 values are adjusted to achieve the desired stable-state relationship for each experimental pCO2 treatment We evaluated the performance of this system in terms of 1) the stability of the parameters of the inorganic carbonate system in all experimental vessels and 2) our ability to successfully rear larvae using these methodologies Our results indicate the suitability of this design for successful manipulation of pCO2 for ocean acidification experiments on larvae

New insights on obtaining phytoplankton concentration and composition from in situ multispectral Chlorophyll fluorescence

Abstract: A three-channel excitation (435 nm, 470 nm, and 532 nm) Chlorophyll fluorometer (695 nm emission) was calibrated and characterized to improve uncertainty in estimated in situ Chlorophyll concentrations. Protocols for reducing sensor-related uncertainties as well as environmental-related uncertainties were developed. Sensor calibrations were performed with thirteen monospecific cultures in the laboratory, grown under limiting and saturating irradiance, and sampled at different growth phases. Resulting uncertainties in the calibration slope induced by natural variations in the in vivo fluorescence per extracted Chlorophyll yield were quantified. Signal variations associated with the sensors (i.e., dark current configurations, drift, and stability) and the environment (i.e., temperature dependent dark currents and contamination by colored dissolved organic matter [CDOM] fluorescence) yielded errors in estimating in situ Chlorophyll concentration exceeding 100%. Calibration protocols and concurrent observations of in situ temperature and CDOM fluorescence eliminate these uncertainties. Depending upon excitation channel, biomass calibration slopes varied between 6- and 10-fold between species and as a function of growth irradiance or growth phase. The largest source of slope variability was due to variations in accessory pigmentation, and thus the variance could be reduced among pigment-based taxonomic lines. Fluorescence ratios were statistically distinct among the pigment-based taxonomic groups, providing not only a means for approximating bulk taxonomic composition, but also for selecting the appropriate calibration slope to statistically improve the accuracy of in situ Chlorophyll concentration estimates. Application to 5 months of deployment in China Lake, Maine, USA reduced the error in estimating extracted Chlorophyll concentration from > 30% to < 6%.

Comparison of objective descriptions of the thermocline

Abstract: Temperature-depth profiles, including the thermocline, are typically described or characterized by mixed layer depth, thermocline depth, and thermocline strength. Objective methods of estimating these parameters are compared with empirical determinations for 200 CTD profiles collected in the eastern and central tropical Pacific, the subtropical North Pacific, and the California Current. The objective methods are (1) maximum slope by difference, (2) maximum slope by regression, (3) four-segment profile model, (4) inflection point, and (5) variable representative isotherm. Mixed layer depth is well estimated by the temperature criterion of (SST-0.8°C) independent of the estimation of thermocline parameters. Thermocline depth and strength are well estimated by the variable representative isotherm method. However, thermocline strength measured as the slope of the temperature-depth profile does not provide a good measure of stratification of the water column. Therefore, it is recommended that the thermocline strength estimate for a profile be supplemented by an estimate of the standard deviation of temperature in the near-surface layer including the thermocline.

Acoustic imaging of natural gas seepage in the North Sea: Sensing bubbles controlled by variable currents

Abstract: Natural seepage from the seafloor is a worldwide phenomenon but quantitative measurements of gas release are rare, and the entire range of the dynamics of gas release in space, time, and strength remains unclear so far. To mitigate this, the hydroacoustic device GasQuant (180 kHz, multibeam) was developed to monitor the tempo-spatial variability of gas bubble releases from the seafloor. GasQuant was deployed in 2005 on the seafloor of the seep field Tommeliten (North Sea) for 36 h. This in situ approach provides much better spatial and temporal resolution of seeps than using conventional ship-born echo sounders. A total of 52 gas vents have been detected. Detailed time series analysis revealed a wide range of gas release patterns ranging from very short periodic up to 50 min long-lasting events. The bulk gas seepage in the studied area is active for more than 70% of observation time. The venting clearly exhibits tidal control showing a peak in the second quarter of the tidal pressure cycle, where pressure drops fastest. The hydroacoustic results are compared with video observations and bubble flux estimates from remotely operated vehicle dives described in the literature. An advanced approach for identifying and visualizing rising bubbles in the sea by hydroacoustics is presented in which water current data were considered. Realizing that bubbles are moved by currents helps to improve the detection of gas bubbles in the data, better discriminate bubbles against fish echoes, and to enhance the S/N ratio in the per se noisy acoustic data.

Application of Solid Phase Adsorption Toxin Tracking (SPATT) for field detection of the hydrophilic phycotoxins domoic acid and saxitoxin in coastal California

Abstract: Recent publications have identified the analysis of phycotoxins in sentinel shellfish as a problematic tool for environmental monitoring purposes. Domoic acid (DA), a neurotoxin produced by some species of the diatom Pseudo-nitzschia, can remain undetected in sentinel shellfish stocks during toxic blooms and subsequent marine bird and mammal mass mortality events. Solid Phase Adsorption Toxin Tracking (SPATT) has previously been described for monitoring of lipophilic toxins, whereas resin-based sampling methods are routinely employed for many other environmental contaminants. Here, we evaluate the applicability of SPATT for monitoring the hydrophilic phycotoxin DA and demonstrate that the same field sampling methods can be used for the detection of saxitoxins. We present laboratory-based adsorption profiles characterizing the performance of SPATT with four resin types: (1) HP20, (2) SP700, (3) SP207, and (4) SP207SS. We present results from 17 mo of approximately weekly SPATT deployments in Monterey Bay, California (USA); this period included two significant toxigenic Pseudo-nitzschia bloom events as well as low-level saxitoxin events. SPATT signaled the presence of DA 3 and 7 weeks before the recognition of bloom conditions by traditional monitoring techniques (7 and 8 weeks before shellfish toxicity). Under ambient (non-bloom) conditions, all resins detected DA when its presence was not apparent from traditional monitoring, highlighting the ubiquity of low level or transient toxin events in the environment. This study is the first to evaluate SPATT deployments in U.S. waters, and the first to demonstrate the applicability of SPATT toward detection of hydrophilic phycotoxins in the field.

Comparison of in situ and satellite-derived (MODIS-Aqua/Terra) methods for assessing temperatures on coral reefs

Abstract: Thermal stress has been regarded as one of the most important parameters monitored on reefs to assess coral health, and therefore, it is important to have accurate temperature data for reef environments Whereas most studies of thermal stress on reefs have relied on sea surface temperature (SST) data, recent findings have suggested that subsurface temperatures may differ considerably from those at the surface We compared concomitant in situ and satellite-derived SST measurements on two different coral reefs off southern Belize Seawater temperatures adjacent to corals at 3 to 5 m depth were measured every 10 to 30 min, from June 2002 to December 2007 An accompanying data set of seawater temperatures was collected every 10 min at 1, 3, 6, 9 and 15 m depth, from October 2006 to December 2007 Concurrent nighttime and daytime SST measurements from MODIS Aqua and Terra platforms with a spatial resolution of 4 km were obtained for comparative purposes Results indicate a negative (cool) bias for remotely sensed SSTs when compared with in situ measurements for both satellites across these two locations Compared with daytime values, nighttime satellite-derived SST measurements yielded larger negative biases and were less correlated with in situ measurements Understanding these biases will not only provide a better evaluation of the thermal regime on individual reefs, but will also create opportunities for more precise temperature comparisons among coral reef environments We stress the importance of “sea-truthing” and complementing satellite-derived SST readings with in situ data when measuring temperatures on coral reefs

An automated pH-controlled culture system for laboratory-based ocean acidification experiments

Abstract: Using a spectrophotometric pH measurement system, an automated 12-tank culture system was developed, which is capable of maintaining pH levels between 7.51 and 8.00 (local, in-situ pH) within 0.02 pH units at 15.1°C. The precise control of pH in the individual culture tanks was achieved through the addition of CO2-enriched seawater to unamended seawater. A feed-back system, which automatically adjusted the mixing ratio of unamended and CO2-enriched seawater, ensured that the pH in each tank was kept within 0.02 pH units of target values. After each tank adjustment, the spectrophotometric pH measurement was combined with a dissolved inorganic carbon measurement to automatically re-calculate carbonate chemistry in each tank. The system was used to study the growth of the geniculate coralline alga Arthrocardia corymbosa at pH levels of 7.52, 7.76, and 7.98.

A comparative study of methods for surface area and three-dimensional shape measurement of coral skeletons

Abstract: The three-dimensional morphology and surface area of organisms such as reef-building corals is central to their biology. Consequently, being able to detect and measure this aspect of corals is critical to understanding their interactions with the surrounding environment. This study explores six different methods of three-dimensional shape and surface area measurements using the range of morphology associated with the Scleractinian corals: Goniopora tenuidens, Acropora intermedia, and Porites cylindrica. Wax dipping; foil wrapping; multi-station convergent photogrammetry that used the naturally occurring optical texture for conjugate point matching; stereo photogrammetry that used projected light to provide optical texture; a handheld laser scanner that employed two cameras and a structured light source; and X-ray computer tomography (CT) scanning were applied to each coral skeleton to determine the spatial resolution of surface detection as well as the accuracy of surface area estimate of each method. Compared with X-ray CT, wax dipping provided the best estimate of the surface area of coral skeletons that had external corallites, regardless of morphological complexity. Foil wrapping consistently showed a large degree of error on all coral morphologies. The photogrammetry and laserscanning solutions were effective only on corals with simple morphologies. The two techniques that used projected lighting were both subject to skeletal light scattering, caused by both gross morphology and meso-coral architecture and which degraded signal triangulation, but otherwise provided solutions with good spatial resolution. X-ray CT scanning provided the highest resolution surface area estimates, detecting surface features smaller than 1000 im2.

Underestimation of rotifer abundance: a much greater problem than previously appreciated

Abstract: Although rotifers are important components of aquatic food webs and suitable sampling methods have been described and tested in the peer-reviewed literature, they are frequently overlooked or quantified with improper methods (e.g., mesh sizes ≥ 63 µm) in freshwater ecology studies. As a result, we believe that the role of rotifers in aquatic food webs and ecosystem processes remains underappreciated, and this conceptual shortfall is exacerbated by the continued use of improper sampling methodology.We examined density and biomass estimates of metazoan zooplankton in the Upper Mississippi and Missouri rivers from two sampling methods. The macrozooplankton method was designed to target cladocerans, adult and juvenile copepods, by filtering 180 L water through a 63-µm mesh. The microzooplankton method was designed to target rotifers and copepod nauplii by filtering 18 L water through a 20-µm mesh. The macrozooplankton method underestimated the density and biomass of common rotifers by two to three orders of magnitude, a far greater amount of error than reported in previous studies. This bias in density estimates for rotifers decreased with increasing mean length of rotifers. The microzooplankton method proved to be ineffective for quantifying cladoceran species richness or cladoceran density at the species level. We urge aquatic ecologists to match their sampling methodology with the specific goals of their study. An accurate understanding of the role of rotifers in freshwater ecosystems will only be possible when the use of appropriate methodology becomes the rule rather than the exception.

Comparison of extraction methods for quantitative analysis of core and intact polar glycerol dialkyl glycerol tetraethers (GDGTs) in environmental samples

Abstract: Archaeal membranes are composed of core lipids called glycerol dialkyl glycerol tetraethers (GDGTs) that contain polar head groups (intact GDGTs) in living cells. The reliability of Archaeal membrane lipids in studies of paleogeochemistry, population distributions, and physiological state depend on efficient extraction and detection of these lipids. We compare existing methods for extraction of core and intact GDGTs so that they can be used as quantitative indicators of living archaeal biomass. We used an active culture of the marine archaeon, Nitrosopumilus maritimus, to document limitations of methods in current use and as a reference for methodological improvement. We found that all extractable GDGTs in the culture were intact and that acid hydrolysis is the only way to quantitatively recover GDGTs from exponentially growing cells. Because acid hydrolysis removes polar head groups, it is not suitable for analysis of intact lipids. In contrast to the culture, high recovery was achieved for intact and core lipids from environmental samples, including water column particles, sediments, and soils. The high recovery from environmental samples and the large portion of core GDGTs relative to intact GDGTs suggest that lipids in the environment are largely derived from dead or dying cells. Because previous studies measured core GDGTs without acid hydrolysis, lipids contained in living cells were not detected and thus these results do not reflect viable biomass. We present a method to accurately quantify living and relict GDGTs by choosing the most efficient extraction protocol and measuring core GDGTs in extracts before and after acid hydrolysis.

Fully automated system for stable isotopic analyses of dissolved nitrous oxide at natural abundance levels

Abstract: Isotopic and isotopomeric analyses of dissolved nitrous oxide (N2O) can provide important information about the mechanisms of production and consumption of this climatically important trace gas. Increased spatial and temporal data coverage for N2O isotopic measurements are needed to improve our understanding of the production of N2O in a variety of aquatic environments, such as coastal and open ocean areas. A new method is presented for automated measurement of δ15Nbulk, δ18O, and site preference of dissolved nitrous oxide in natural waters using a GC-Pal autosampler and a Finnigan DeltaPlus isotope ratio mass spectrometer and is capable of analyzing 30 samples in 22 h without user attention after the start of the run. The system was first tested with samples produced by injecting our N2O reference gas and/or N2O test mixtures, ranging in isotopic composition and concentration, into N2-sparged seawater. The method was then applied to samples containing a large range of N2O concentrations, δ15Nbulk, δ18O, and site preference values from two high-resolution depth profiles from the Arabian Sea. The results showed precise determination of isotopic values of N2O from 160 mL aqueous samples over the concentration range normally found in the oceans (5–80 nmol L−1). Sample standard deviation for triplicate 160 mL samples at 6 nmol L−1 N2O is better than 0.3‰ for δ15Nbulk, 0.5‰for δ18O, and 1.0‰ for 15N site preference. The automated technique described here requires relatively minor modifications of existing N2O purge and trap systems and can be implemented broadly for a variety of applications.

A novel method to measure particle sinking velocity in vitro, and its comparison to three other in vitro methods

Abstract: We introduce a novel, simple method to measure sinking velocity of particles and aggregates in roller tanks. Using this noninvasive method, it is possible to follow changes in sinking velocities on the same aggregates during time and to make paired measurements of aggregate sinking velocity and composition. Particles and aggregates are video recorded in roller tanks, and their sinking velocity is derived from the orbital trajectories. This new method is compared with three other methods (using roller tanks, a vertical flow system, and a sedimentation column), which have not previously been inter-calibrated. Agar spheres and diatom aggregates were used as model particles in all experimental systems. No method showed significantly different sinking velocities of agar spheres compared with those calculated by theory. Paired measurements showed that sinking velocities from 70 to 700 m d(-1) were linearly correlated between different methods. Highest sinking velocities were measured in a sedimentation column followed by those measured in roller tanks and in the vertical flow system, respectively. The average difference of sinking velocity measured with the different methods ranged from 8% to 11% for agar spheres, and up to 20% for diatom aggregates.

Mobile autonomous process sampling within coastal ocean observing systems

Abstract: Predicting when and where key oceanic processes will be encountered is problematic in dynamic coastal waters where diverse physical, chemical, and biological factors interact in varied and rapidly changing combinations. Defining key processes often requires efficient sampling of specific water masses and prompt sample return for subsequent analyses. This compound challenge motivated our efforts to develop mobile autonomous process sampling (MAPS) for use with autonomous underwater vehicles (AUVs). With this system, features are recognized by artificial intelligence that integrates AUV sensor data to estimate probabilistic states for adaptive control of survey navigation and triggering of targeted water samplers. To demonstrate the utility of the MAPS/AUV system, we focused on intermediate nepheloid layers (INLs), episodic transport events that may play a role in zooplankton ecology. During multiple field tests in Monterey Bay, California, the MAPS/AUV system recognized, mapped, and sampled INLs. Invertebrate larvae contained in the water samples were subsequently characterized with molecular probes developed for high-throughput screening. Preliminary results support the hypothesis that INLs function as vehicles for episodic larval transport. Applying MAPS within a greater coastal ocean observing system permitted description of regional oceanographic dynamics that influenced the patterns and scales of INL and larval transport.

Toward continuous monitoring of seawater 13CO2/12CO2 isotope ratio and pCO2: Performance of cavity ringdown spectroscopy and gas matrix effects

Abstract: The potential of a continuous wave cavity ringdown spectrometer for monitoring the isotope ratio 13CO2/12CO2 and the partial pressure pCO2 of CO2 dissolved in water was thoroughly analyzed by quantitative measurements. Running calibration gas standards under typical operation conditions, a relative accuracy of D(d13C[CO2]) = ±0.1‰ with 120 min averaging time has been demonstrated. Absolute uncertainties were determined to be D(d13C[CO2]) = ±0.2‰ and D(xCO2) = ±0.5 ppmv. No principle problems were encountered when using the instrument in combination with a water-air equilibration setup. By contrast, when performing measurements of CO2 in gas matrices with a composition different from that of ambient air, pressure broadening linewidth effects induced significant errors in both d13C(CO2) and xCO2 values. These effects, which compromise the accessible accuracy in environmental studies, can be quantitatively taken into account by using a spectroscopically based correction procedure. Relying on linewidth analysis, the instrument was shown to be capable of continuous and simultaneous measurement of d13C(CO2), pCO2, as well as water content and O2 supersaturation, and thus holds the potential for online monitoring of these quantities aboard research vessels.

Evaluating oxygen fluxes using microprofiles from both sides of the sediment‐water interface

Abstract: Sediment-water fluxes are influenced by both hydrodynamics and sediment biogeochemical processes. However, fluxes at the sediment-water interface (SWI) are almost always analyzed from either a water-or sediment-side perspective. This study expands on previous work by comparing water-side (hydrodynamics and resulting diffusive boundary layer thickness, delta(DBL)) and sediment-side (oxygen consumption and resulting sediment oxic zone) approaches for evaluating diffusive sediment oxygen uptake rate (J(O2)) and delta DBL from microprofiles. Dissolved oxygen microprofile and current velocity data were analyzed using five common methods to estimate J(O2) and delta(DBL) and to assess the robustness of the approaches. Comparable values for J(O2) and delta(DBL) were obtained (agreement within 20%), and turbulence-induced variations in these parameters were uniformly characterized with the five methods. J(O2) estimates based on water-side data were consistently higher (+1.8 mmol m(-2) d(-1) or 25% on average) and delta(DBL) estimates correspondingly lower (-0.4 mm or 35% on average) than those obtained using sediment-side data. This deviation may be attributed to definition of the sediment-water interface location, artifacts of the methods themselves, assumptions made on sediment properties, and/or variability in sediment oxygen-uptake processes. Our work emphasizes that sediment-side microprofile data may more accurately describe oxygen uptake at a particular location, whereas water-side data are representative of oxygen uptake over a broader sediment area. Regardless, our overall results show clearly that estimates of J(O2) and delta(DBL) are not strongly dependent on the method chosen for analysis.

Determination of total dissolved cobalt in UV-irradiated seawater using flow injection with chemiluminescence detection

Abstract: A sensitive flow-injection method with chemiluminescence detection (FI-CL) for the determination of dissolved cobalt in open ocean samples, suitable for shipboard use has been developed. To date, FI methods for dissolved cobalt have been used only in coastal and estuarine waters. Therefore, significant modifications to existing methods were required, including (1) the use of a commercially available iminodiacetate (IDA) resin (Toyopearl AF-chelate 650M) in place of resin immobilized 8-hydroxyquinoline for online preconcentration and matrix removal, (2) the introduction of acidified ammonium acetate (pH 4) as a column-conditioning step before sample loading and rinse steps, and most importantly, (3) UV irradiation of acidified seawater samples to determine total dissolved cobalt, rather than an operationally defined fraction. This method had a detection limit of 4.5 pM (3σ of the blank). The accuracy of the method was evaluated by determining total dissolved cobalt in acidified North Pacific deep seawater (1000 m) samples from the Sampling and Analysis of Iron (SAFe) program and NASS-5. The method yields a mean (± SD) value of 40.9 ± 2.6 pM (n = 9), which is in excellent agreement with the SAFe consensus value of 43 ± 4 pM, and 208 ± 30 pM for NASS-5 (certified value 187 ± 51 pM). This study demonstrates that UV irradiation is an essential step for the determination of total dissolved cobalt in seawater by FI-CL. The method was applied to vertical profiles from the Sargasso Sea, indicating that total dissolved cobalt is influenced by both biological and physical processes.

Damage and recovery assessment of vessel grounding injuries on coral reef habitats by use of georeferenced landscape video mosaics

Abstract: Vessel groundings are a major source of disturbance to coral reefs worldwide. Documenting the extent of damage caused by groundings is a crucial first step in the reef restoration process. Here, we describe the application of a novel survey methodology, landscape video mosaics, to assessment of the damage caused by vessel groundings. Video mosaics, created by merging thousands of video frames, combine quantitative and qualitative aspects of damage assessment and provide a georeferenced, landscape, high-resolution, spatially accurate permanent record of an injury. The scar in a Florida reef impacted by a 49-foot vessel, imaged in 2005 and 2006, covered an area of 150 m2 (total imaged area was >600 m2). The impacted coral community showed limited signs of coral recovery more than 3 years after the initial impact; the cover of corals was still significantly higher in the undamaged areas compared to the scar. However, seagrass colonization of the scar was observed. Finally, no evidence of further physical impacts was documented even when four hurricanes passed near the grounding site in 2005. The video mosaics developed in this study proved to be ideal tools to survey the grounding scars. Mosaics provide a means to collect information on the size of the damage area and the status and trends of the impacted biological communities and provide a permanent visual record of the damage, thereby expanding the quality and diversity of information that can be collected during field surveys.

A low-cost automated trap to measure bubbling gas fluxes

Abstract: We describe a trap that can be used for automated, high temporal resolution measurement of ebullition fluxes in aquatic environments. The trap comprises a submerged cone connected to a transparent PVC pipe that serves as a collection chamber. A differential pressure sensor at the top of the pipe measures the pressure caused by gas accumulation in the chamber. The sensor circuit consists of low-power electronics and can function for longer than 6 months on two high-capacity AA lithium batteries. The circuit, batteries, and a commercial data logger that records the measurements are enclosed in a custom-made, 10-cm diameter waterproof housing. The trap is designed to be fabricated economically and easily so that many units can be deployed for greater spatial coverage. We have used several of these automated traps to measure bubbling fluxes at a lake, and have collected data continuously at a resolution of 5 or 10 min over 6 months.

Total carbon analysis may overestimate organic carbon content of fresh waters in the presence of high dissolved inorganic carbon

Abstract: Automated carbon analyzers often are configured to provide estimates of both total organic carbon (TOC) and nonpurgeable organic carbon (NPOC) We show there can be an overestimation of total carbon in the presence of moderate to large quantities of dissolved inorganic carbon This leads to overestimates of TOC, which is measured as the difference between total carbon and inorganic carbon Water samples were analyzed as both TOC and NPOC on a Shimadzu TC 5050 Carbon Analyzer The difference between TOC and NPOC increased as a function of concentrations of dissolved inorganic carbon (DIC) Water samples spiked with DIC ranging from 0 to 100 mg DIC/L also reported increased TOC as large as 8 mg C/L Our data suggest that the Shimadzu 5050 analyzer (and by analogy other instruments that estimate TOC by difference between TC and IC) overestimates total carbon (TC) when calibrated with an organic standard as recommended by the manufacturer The magnitude of the overestimation varies both with the amount of DIC present in the sample and the extent to which measurement efficiency of the analyzer is less than 100% The consequences will be most severe in analysis of samples from systems spanning a large range in DIC Time series from individual systems are less likely to be affected because the necessary large change in DIC would be detected as changes in pH or other attributes well before any change in DOC Systems with high DIC will, however, be susceptible to even small variations in measurement efficiency

Methods for rearing the invasive zooplankter Bythotrephes in the laboratory

Abstract: The invasive spiny water flea's (Bythotrephes longimanus) current North American distribution encompasses the Laurentian Great Lakes as well as a number of inland lakes, particularly on the Canadian Shield. In the past, poor survival in the laboratory has precluded controlled long-term studies on Bythotrephes. Here we investigated field collection techniques and choices of culture media, temperature, and diet that led to the successful maintenance of Bythotrephes from birth to reproduction. Gravid parthenogenic females were collected from invaded lakes. Resulting offspring were reared in source lake water filtered through 20 or 80 µm, or a fully defined artificial culture medium, FLAMES. Individuals raised in FLAMES produced significantly larger broods than those in lake water, indicating that it is an appropriate culture medium. We next conducted a 96-h temperature bioassay on juvenile Bythotrephes. Survival was comparable at 16°C, 20°C, and 24°C but decreased after 48 h at 28°C, and most animals died after 24 h at 32°C. We also reared Bythotrephes at 16°C, 19°C, 22°C, and 25°C. Corresponding intrinsic rates of natural increase (r) for animals maintained to first brood release were 0.02, 0.05, 0.06, and 0.03 d−1, suggesting that Bythotrephes should be reared at ~22°C to benefit from maximum population increases. Feeding trials confirmed that young Bythotrephes prefer small, slow-moving prey. Finally, we devised a protocol for rearing Bythotrephes that yielded 100% survival to reproduction and r = 0.10 d−1 (for animals maintained to first brood release). Given these results, it is now possible to conduct long-term laboratory studies on this invader.

Calculating density of water in geochemical lake stratification models

Abstract: To model chemically stratified lakes numerically, chemical transformations must be reflected in the density function. In this contribution, partial molal volumes are used to calculate density from the chemical composition of lake water. Such values have been evaluated for cations and anions separately, to facilitate an easy implementation into geochemical stratification models for lakes. Coefficients for temperature dependence and variation for higher ionic strengths were evaluated from previously published data. An algorithm RHOMV to calculate density with a second order approximation for temperature dependence and ionic strength dependence is proposed. The accuracy is tested for seawater composition. We conclude that this approach delivers a representation of density based on the actual chemical composition of the lake water, which is accurate enough for most limnological purposes. The implementation of RHOMV into geochemical stratification models facilitates the numerical tackling of pressing questions, such as meromixis or double diffusive features or altered circulation patterns of lakes due to changing climate or change of use.