Diatoms favor their younger daughters
Laney, S. R., R. J. Olson, and H. M. Sosik. 2012
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.
Limnol. Oceanogr. 57, 1572-1578.
Massive phytoplankton blooms under Arctic sea iceArrigo, 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 transientsLaney, 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 OceanTimmermans, 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 levelS. 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 fluorometryS. 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 bacterioplanktonDesiderio, 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 SAR11Giovannoni, 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 weissflogiiLaney, 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 applicationsLaney, 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 fluorometryLaney, 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 culturesLaney, 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 fluorescenceLaney, S. R., 1997
Sea Technology 38, 99-102