Selected Publications

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The euphotic zone under Arctic Ocean sea ice: vertical extents and seasonal trends

Laney, S. R., R. A. Krishfield, and J. M. Toole. 2017. Limnol. Oceanogr. in press.

Eight Ice-Tethered Profilers were deployed in the Arctic Ocean between 2011 and 2013 to measure vertical distributions of photosynthetically active radiation (PAR) and other bio-optical properties in ice-covered water columns, multiple times a day over periods of up to a year. With the radiometers used on these profilers, PAR could be measured to depths of only ∼20–40 m in the central Arctic in late summer under sea ice ∼1 m thick. At lower latitudes in the Beaufort Gyre, late summer PAR was measurable under ice to depths exceeding 125 m. The maximum depths of measurable PAR followed seasonal trends in insolation, with isolumes shoaling in the fall as solar elevation decreased and deepening in spring and early summer after insolation resumed and sea ice diminished. PAR intensities were often anomalously low above 20 m, likely due to a shading effect associated with local horizontal heterogeneity in light transmittance by the overlying sea ice. A model was developed to parameterize these complex vertical PAR distributions to improve estimates of the water column diffuse attenuation coefficient and other related parameters. Such a model is necessary to separate the effect of surface ice heterogeneity on under-ice PAR profiles from that of the water column itself, so that euphotic zone depth in ice-covered water columns can be computed using canonical metrics such as the 1% light level. Water column diffuse attenuation coefficients derived from such autonomously-collected PAR profile data, using this model, agreed favorably with values determined manually in complementary studies.

A general-purpose, microcontroller-based framework for integrating oceanographic sensors, instruments, and peripherals

Laney, S. R. 2017.  J. Atmos. Ocean. Tech. 34, 415-427.

Sensors and instruments for basic oceanographic properties are becoming increasingly sophisticated, which both simplifies and complicates their use in field studies. This increased sophistication disproportionately affects smaller-scale observational efforts that are less likely to be well supported technically but which need to integrate instruments, sensors, and commonly-needed peripheral devices in ways not envisioned by their manufacturers. A general-purpose hardware and software framework was developed around a widely-used family of low-power microcontrollers to lessen the technical expertise and customization required to integrate sensors, instruments, and peripherals and thus simplify such integration scenarios. The hardware and associated firmware development tools both provide a range of features often required in such scenarios: serial data interfaces, analog inputs and outputs, logic lines and power switching capability, nonvolatile storage of data and parameters for sampling or configuration, and serial communication interfaces to supervisory or telemetry systems. The microcontroller and additional components needed to implement this integration framework are small enough to encapsulate in standard cable splices, creating a small form factor “smart cable” that can be readily wired and programmed for a range of integration needs. An application programming library developed for this hardware provides skeleton code for functions commonly desired when integrating sensors, instruments, and peripherals. This minimizes the firmware programming expertise needed to apply this framework in many integration scenarios and thus streamlines the development of firmware for different field applications. Envisioned applications are in field programs where significant technical instrumentation expertise is unavailable or not cost effective.

A Fiber Optic Spectrometry System for Measuring Irradiance Distributions in Sea Ice Environments

Wang, H.*, Chen, Y., Song, H., and Laney, S. R. 2014
J. Atmos. Oce. Tech. 31, 2833-2857.

*Student member of Laney lab

A fiber optic–based spectrometry system was developed to enable automated, long-term measurements of spectral irradiance in sea ice environments. This system utilizes a single spectrometer module that measures the irradiance transmitted by multiple optical fibers, each coupled to the input fiber of the module via a mechanical rotary multiplexer. Small custom-printed optical diffusers, fixed to the input end of each fiber, allow these probes to be frozen into ice auger holes as small as 5 cm in diameter. Temperature-dependent biases in the spectrometer module and associated electronics were examined down to 2408C using an environmental chamber to identify any artifacts that might arise when operating these electronic and optical components below their vendor-defined lower temperature limits. The optical performance of the entire system was assessed by freezing multiple fiber probes in a 1.2-m-tall ice column, illuminating from above with a light source, and measuring spectral irradiance distributions at different depths within the ice column. Results indicated that the radiometric sensitivity of this fiber-based system is comparable to that of commercially available oceanographic spectroradiometers.

Correcting temperature dependence in miniature spectrometers used in cold polar environments

Wang, H.*, Chen, Y., Song, H., and Laney, S. R. 2015
Appl. Optics. 54, 3162-3172.

*Student member of Laney lab

Measurement biases arising from changes in temperature can be a major concern when using miniature spectrometers in extreme environments, particularly when temperature stabilization approaches are not feasible. Here, temperature-related biases of a low-power field spectrometry system comprised of a CMOS miniature monolithic spectrometer module and custom driver electronics were examined between −40°C and 25.6°C, well below the stated operating range of this particular spectrometer. Using these observations, a predictive model was developed to estimate the dark output of the spectrometry system within this extended operating range. This information was used to correct the signal at any measured integration time and temperature to that which would be measured at a reference integration time and temperature. This approach provides a general framework for assessing the temperature dependence of monolithic spectrometers whose field use will occur at temperatures outside of the range examined by the

Phytoplankton assemblage structure in and around a massive under-ice bloom in the Chukchi Sea

Laney, S. R., and H. M. Sosik. 2014
Deep-Sea Res. II 105, 30-41.

Standard and imaging flow cytometry were used to examine the composition of phytoplankton assemblages in and around a massive under-ice bloom in the Chukchi Sea in 2011. In the core of this bloom, roughly 100 km northwest of Hanna Shoal, diatoms represented roughly 87% of the water column carbon-specific biomass of phytoplankton, while nanophytoplankton contributed ~9%. Picoeukaryotes were also observed in this bloom, as were phycoerythrin-containing cells consistent with Synechococcus spp., but picophytoplankton, dinoflagellates, and prymnesiophytes each represented only ~1% of the bloom's phytoplankton biomass. More broadly along this part of the Chukchi shelf, nanophytoplankton typically comprised a larger fraction of phytoplankton biomass in the water column, 22% on average but up to 82% at certain locations. Dinoflagellates and prymnesiophytes contributed at most 2% of water column biomass at any location and were most abundant in the deeper slope stations northeast of Hanna Shoal, east of the bloom. Picophytoplankton were most abundant in these deeper slope stations as well, and also in recently ice-free areas to the south around Hanna Shoal. These cell-derived estimates of phytoplankton carbon biomass, which were computed from imaging and standard cytometric observations of phytoplankton cell sizes and from published carbon:volume relationships, agree well with independent measurements of particulate organic carbon concentration from traditional biochemical assays.

Phytoplankton blooms beneath the sea ice in the Chukchi sea

Kevin R. Arrigo, Donald K. Perovichb, Robert S. Pickart, Zachary W. Brown, Gert L. van Dijken, Kate E. Lowry, Matthew M. Mills, Molly A. Palmer, William M. Balch, Nicholas R. Bates, Claudia R. Benitez-Nelson, Emily Brownlee, Karen E. Frey, Samuel R. Laney, Jeremy Mathis, Atsushi Matsuoka, B. Greg Mitchell, G.W.K. Moore,    Rick A. Reynolds, Heidi M. Sosik, James H. Swift, 2014
Deep-Sea Res. II 105, 1-16.

In the Arctic Ocean, phytoplankton blooms on continental shelves are often limited by light availability, and are therefore thought to be restricted to waters free of sea ice. During July 2011 in the Chukchi Sea, a large phytoplankton bloom was observed beneath fully consolidated pack ice and extended from the ice edge to >100 km into the pack. The bloom was composed primarily of diatoms, with biomass reaching 1291 mg chlorophyll a m−2 and rates of carbon fixation as high as 3.7 g C m−2 d−1. Although the sea ice where the bloom was observed was near 100% concentration and 0.8–1.2 m thick, 30–40% of its surface was covered by melt ponds that transmitted 4-fold more light than adjacent areas of bare ice, providing sufficient light for phytoplankton to bloom. Phytoplankton growth rates associated with the under-ice bloom averaged 0.9 d−1 and were as high as 1.6 d−1. We argue that a thinning sea ice cover with more numerous melt ponds over the past decade has enhanced light penetration through the sea ice into the upper water column, favoring the development of these blooms. These observations, coupled with additional biogeochemical evidence, suggest that phytoplankton blooms are currently widespread on nutrient-rich Arctic continental shelves and that satellite-based estimates of annual primary production in waters where under-ice blooms develop are ~10-fold too low. These massive phytoplankton blooms represent a marked shift in our understanding of Arctic marine ecosystems.

Assessing algal biomass and bio-optical distributions in perennially ice-covered polar ocean ecosystems

Laney, S. R., R. A. Krishfield, J. M. Toole, T. R. Hammar, C. J. Ashjian, and M.-L. Timmermans, 2014
Polar Sci. 8, 73-85.

Under-ice observations of algal biomass and seasonality are critical for understanding better how climate-driven changes affect polar ocean ecosystems. However, seasonal and interannual variability in algal biomass has been studied sparsely in perennially ice-covered polar ocean regions. To address this gap in polar ocean observing, bio-optical sensors for measuring chlorophyll fluorescence, optical scattering, dissolved organic matter fluorescence, and incident solar radiation were integrated into Ice-Tethered Profilers (ITPs). Eight such systems have been deployed in the Arctic Ocean, with five profilers completing their deployments to date including two that observed an entire annual cycle in the central Arctic Ocean and Beaufort Sea respectively. These time series revealed basic seasonal differences in the vertical distributions of algal biomass and related bio-optical properties in these two regions of the Arctic Ocean. Because they conduct profiles on daily or sub-daily scales, ITP bio-optical data allow more accurate assessments of the timing of changes in under-ice algal biomass such as the onset of the growing season in the water column, the subsequent export of particulate organic matter at the end, and the frequency of intermittent perturbations, which in the central Arctic Ocean were observed to have time scales of between one and two weeks.

Diatoms favor their younger daughters

Laney, S. R., R. J. Olson, and H. M. Sosik. 2012
Limnol. Oceanogr. 57, 1572-1578.

We used a time-lapse imaging approach to examine cell division in the marine centric diatom Ditylum brightwellii and observed that daughter cells who inherited their parents’ hypothecal frustule half were more likely to divide before their sisters. This is consistent with observations in Escherichia coli of a bias between sister cells, where faster growth in one sister is thought to arise from its inheriting parental material with less oxidative damage. We also observed that hypothecal sisters in D. brightwellii were more likely to inherit a greater proportion of their parents’ cellular material, similar to what has been seen in E. coli. We found a statistically significant correlation between the amount of parental material inherited by a hypothecal daughter and its relative division rate, indicating that this extra material inherited by the hypothecal daughter plays a role in its more rapid division. Furthermore, the intercept in this regression was greater than zero, indicating that other factors, such as differences in the quality of inherited material, also play a role. This similarity between two taxonomically distant microbes suggests that favoritism toward one daughter might occur broadly among unicellular organisms that reproduce asexually by binary fission. Such a bias in cell division might be advantageous, given model predictions that show that favoring one daughter at the expense of the other can result in higher population growth rates, increasing the chance that a cell’s genotype will survive compared to a model where the daughters divide at equal rates.

Massive phytoplankton blooms under Arctic sea ice

Arrigo, K. R., D. K. Perovich, R. S. Pickart, Z. W. Brown, G. L. van Dijken, K. E. Lowry, M. M. Mills, M. A. Palmer, W. B. Balch, F. Bahr, N. R. Bates, C. Benitez-Nelson, B. Bowler, E. Brownlee, J. K. Ehn, K. E. Frey, R. Garley, S. R. Laney, L. Lubelczyk, J. Mathis, A. Matsuoka, B. G. Mitchell, G. W. K. Moore, E. Ortega-Retuerta, S. Pal, C. M. Polashenski, R. A. Reynolds, B. Schieber, H. M. Sosik, M. Stephens, J. H. Swift. 2012
Science 336, 1408

During the 2011 ICESCAPE (Impacts of Climate on EcoSystems and Chemistry of the Arctic Pacific Environment) cruise, we observed a massive phytoplankton bloom that had developed beneath the 0.8- to 1.3-m thick first-year sea ice on the Chukchi Sea continental shelf.

In situ measurement of chlorophyll fluorescence transients

Laney, S. R. 2010
Developments in Applied Phycology 4, 19-30.

Chlorophyll variable fluorescence provides considerable insight into the photosynthetic physiology of plants and algae, in particular the structure and function of Photosystem II (PSII). This chapter outlines the nuances of working with active fluorescence methods in situ in marine environments.

Ice-Tethered Profiler measurements of dissolved oxygen under permanent ice cover in the Arctic Ocean

Timmermans, M.-L., R. Krishfield, S. Laney, and J. Toole, 2010
J. Atmos. Ocean. Tech. 27, 1936–1949

Four ice-tethered profilers (ITPs), deployed between 2006 and 2009, have provided year-round dissolved oxygen (DO) measurements from the surface mixed layer to 760-m depth under the permanent sea ice cover in the Arctic Ocean. These ITPs drifted with the permanent ice pack and returned 2 one-way profiles per day of temperature, salinity, and DO. Long-term calibration drift of the oxygen sensor can be characterized and removed by referencing to recently calibrated ship DO observations on deep isotherms. Observed changes in the water column time series are due to both drift of the ITP into different water masses and seasonal variability, driven by both physical and biological processes within the water column. Several scientific examples are highlighted that demonstrate the considerable potential for sustained ITP-based DO measurements to better understand the Arctic Ocean circulation patterns and biogeochemical processes beneath the sea ice.

Using a nonanalytical approach to model nonlinear dynamics in photosynthesis at the photosystem level

S. R. Laney, R. M. Letelier, and M. R. Abbott, 2009
J. Phycol. 45, 298–310

Nonlinear dynamics in photon capture and uptake at the photosystem level may have a strong effect on photosynthetic yield. However, the magnitude of such effects is difficult to estimate theoretically because nonlinear systems often cannot be represented accurately using equations. A nonanalytical simulation was developed that used a simple decision tree and Monte Carlo methods, instead of equations, to model how a population of photosystems absorbs and utilizes photons from an ambient light field. This simulation replicated realistic kinetics in the closure and variable fluorescence yield of Photosystem II on the single-turnover time scale, as well as the saturating behavior in light-driven electron flow that is observed in nature with increasing irradiance. This simulation indicated that the transfer of absorbed photon energy among Photosystem II can introduce strong nonlinear enhancement in light-driven electron flow. Yet this effect was seen only in populations with particular photosynthetic states as determined by physiological properties of Photosystem II. Other populations with the same degree of energy transfer but with different photosynthetic states exhibited little enhancement in electron flow, and in some cases a reduction. This nonanalytical approach provides a simple means to quantify theoretically how nonlinear dynamics in photosynthesis arise at the photosystem level and how these dynamics may act to enhance or constrain photosynthetic rates and yields. Such simulations can provide quantitative insight into different physiological bases of nonlinear light harvesting dynamics and identify those that would have the strongest theoretical influence and thus warrant closer experimental examination.

Artifacts in measurements of chlorophyll fluorescence transients, with specific application to fast repetition rate fluorometry

S. R. Laney and R. M. Letelier, 2008
Limnol. Oceanogr.: Meth. 6, 40-50

A theoretical framework was developed to describe how instrument and sample artifacts affect measurements of variable fluorescence transients in phytoplankton. This framework identified the proper procedure for correcting for common artifacts in the transients measured with a widely used instrument, the Fasttracka fast repetition rate fluorometer. The impulse response of this fluorometer can be substantial, requiring correction for a dynamic instrument artifact in addition to the static artifacts that can be assessed using traditional “blanks.” In a low-biomass region of the North Pacific, approximately one-third of the fluorescence transient measured with this instrument represented such artifacts. Correcting for these using filtered seawater blanks only, and not accounting for the instrument’s own response, failed to remove errors as high as 22% in estimates in the photochemical yield and as much as –16% to +22% in estimates of the functional cross section of Photosystem II. This analytical framework and the corrective procedure are generalized and can be used to determine how a wide range of artifacts affect measured variable fluorescence transients, including those characteristic of fluorometers other than the Fasttracka or those more relevant in meso- or eutrophic regions of the ocean.

Using lasers to probe the transient light absorption by proteorhodopsin in marine bacterioplankton

Desiderio, R. A., S. R. Laney, R. M. Letelier, and S. J. Giovannoni, 2007
Appl. Optics 46, 7329-7336

We constructed an experimental apparatus that used lasers to provide the probe beams for measuring the transient absorption kinetics of bacterioplankton that contain proteorhodopsin, a microbial protein that binds retinal and is analogous to animal rhodopsin. With this approach we were able to observe photocycles characteristic of functioning retinylidene ion pumps. Using light from lasers instead of broadband sources as transmittance probe beams can be advantageous when examining optically dense, highly scattering samples such as concentrated microbial cultures. Such a laser-based approach may prove useful in shipboard studies for identifying proteorhodopsin in whole cell suspensions concentrated from seawater.

Proteorhodopsin phototrophy in the ubiquitous marine bacterium SAR11

Giovannoni, S. J., L. Bibbs, J.-C. Cho, M. D. Stapels, R. Desiderio, K. Vergin, M. S. Rappe, S. Laney, L. J. Wilhelm, H. J. Tripp, E. J. Mathur, and D. F. Barofsky, 2005
Nature 438, 82-85

Proteorhodopsins are light-dependent proton pumps that are predicted to have an important role in the ecology of the oceans by supplying energy for microbial metabolism. Proteorhodopsin genes were first discovered through the cloning and sequencing of large genomic DNA fragments from seawater. They were later shown to be widely distributed, phylogenetically diverse, and active in the oceans. Proteorhodopsin genes have not been found in cultured bacteria, and on the basis of environmental sequence data, it has not yet been possible to reconstruct the genomes of uncultured bacterial strains that have proteorhodopsin genes. Although the metabolic effect of proteorhodopsins is uncertain, they are thought to function in cells for which the primary mode of metabolism is the heterotrophic assimilation of dissolved organic carbon. Here we report that SAR11 strainHTCC1062 (‘Pelagibacter ubique), the first cultivated member of the extraordinarily abundant SAR11 clade, expresses a proteorhodopsin gene when cultured in autoclaved seawater and in its natural environment, the ocean. The Pelagibacter proteorhodopsin functions as a light-dependent proton pump. The gene is expressed by cells grown in either diurnal light or in darkness, and there is no difference between the growth rates or cell yields of cultures grown in light or darkness.

Parameterizing the natural fluorescence kinetics of Thalassiosira weissflogii

Laney, S. R., R. M. Letelier, and M. R. Abbott, 2005
Limnol. Oceanogr. 50, 1499-1510.

We examined variability in the natural fluorescence yield of a neritic diatom, Thalassiosira weissflogii, in continuous cultures. In this species, kinetics in natural fluorescence yield over time scales less than a photoperiod were characterized by sharp decreases, occurring at irradiance intensities that presumably coincide with the onset of nonphotochemical fluorescence quenching by interconvertible xanthophylls. The irradiance at which these decreases occurred, and the concomitant degree of quenching involved, varied systematically in these cultures as a function of dilution rate and irradiance intensity, independent of biomass. Similar diurnal kinetics in natural fluorescence yield were observed in phytoplankton assemblages in a coastal transition region in the Gulf of Alaska. An empirical parameterization was developed to quantify these diurnal kinetics in terms of the magnitude of this increased quenching and the irradiance at which it occurred, in order to track the behavior of these kinetics over longer time scales of days to weeks.

A generalized real-time signal processor for oceanographic applications

Laney, S. R., 2005
Research Papers of the Link Foundation Fellows 4, B. J. Thompson, ed., pp. 333-349.

Biological oceanographic instruments, especially those designed for in situ deployments, are continually increasing in sophistication. For example, chlorophyll fluorometers, which only a decade ago output a single analog voltage, now generate multi-parameter digital data streams at high rates and with complex output formats. Such sensors in turn place greater demands on systems required to monitor, log, or transmit these data streams. This problem is particularly acute when interfacing such sensors to independent oceanographic platforms like moorings, drifters, autonomous vehicles, or animal tags, since these platforms often have limited data storage and telemetry capabilities due to heavy optimization for power consumption, weight, and space. Advances in digital signal processing hardware and algorithms now make it feasible to conduct a wide range of signal processing operations on oceanographic data in real time, in situ, using very low power microprocessors. Such methods provide a means to parse, transform, compress, filter, or quality check complex data streams before these are presented to logging or telemetry systems. Such inline data processing minimizes the demands these complex sensors place on autonomous platforms. A generalized, programmable digital signal processing module was developed that can be programmed to perform a wide range of signal processing operations in situ and in real time. This paper describes one application of this signal processing module, where it was interfaced to a self-contained animal tag and configured to sample the metabolic heat flux of a right whale. Heat flux and temperature gradient data collected during field deployments were characterized. Signal processing algorithms suitable for real time signal processing using this module were evaluated for future use in similar studies.

Assessing the error in photosynthetic properties determined with Fast Repetition Rate fluorometry

Laney, S. R.
Limnol. Oceanogr. 48, 2234-2242

Fast repetition rate (FRR) fluorometry is an optical technique for estimating photosynthetic properties of phytoplankton from measurements of variable fluorescence yield. I determined the minimum error in such estimates contributed by inherent instrument biases, improper measurement protocols, and the type of optimization algorithm used to infer photosynthetic variability from changes in variable fluorescence. Many of these errors were nonrandom in origin and would not be reduced with repeated sampling or averaging. Characterization of a commercial FRR fluorometer (FRRF) showed undocumented hardware biases with magnitudes roughly equivalent to those addressed by the current characterization approach. Robust optimization algorithms were less likely to misidentify these biases as representing actual photosynthetic variability. In general, robust algorithms improved the accuracy, precision, and distribution of error in analyses of both simulated and actual variable fluorescence measurements. When reanalyzed with robust algorithms, in situ data from an FRRF indicated different photosynthetic behavior than did the analysis tool used originally. Methods to improve and standardize the collection and analysis of FRR variable fluorescence data are essential for evaluating the strengths and limitations of this powerful, but involved, technique. Although the error minimization procedures described were developed primarily to minimize errors and artifacts with FRR fluorometry, several are generally applicable to any fluorescence yield technique in which a physiological model is used to estimate photosynthetic parameters from variable fluorescence measurements.

Measuring the natural fluorescence of phytoplankton cultures

Laney, S. R., R. M. Letelier, R. A. Desiderio, D. A.. Kiefer, C. R. Booth, and M. R. Abbott. 2001.
J. Atmos. Ocean. Tech. 18, 1924-1934.

A laboratory instrument, the Natural Fluorescence Chemostat, was developed to measure the natural fluorescence of phytoplankton cultures. With this instrument, the physical and chemical environment of a culture can be manipulated with respect to temperature, pH, nutrient delivery rate, and light intensity, while the natural fluorescence and a weak stimulated fluorescence are continuously recorded with high temporal resolution. The geometry and spectral distribution of the artificial light field minimize the contribution of scattering to the natural fluorescence signal. Preliminary investigations with the marine diatom T. weissflogii (Bacillariophyceae) indicate that the instrument can detect natural fluorescence signals in broadband artificial light fields as bright as 1250 μmol quanta m-2 s-1. Since the influence of environmental factors on natural fluorescence is not well understood, laboratory experiments are essential for investigating how ocean physics and chemistry influence this signal. This instrument provides a quantitative means to examine how the magnitude and kinetics of phytoplankton natural fluorescence vary in response to changes in the physical and chemical environment.

Fast Repetition Rate fluorometry - Exploring phytoplankton fluorescence

Laney, S. R., 1997
Sea Technology 38, 99-102


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